diff --git a/src/main/java/picard/util/IntervalList/IntervalListScatterMode.java b/src/main/java/picard/util/IntervalList/IntervalListScatterMode.java index 545bb8cf7a..126d2b9647 100644 --- a/src/main/java/picard/util/IntervalList/IntervalListScatterMode.java +++ b/src/main/java/picard/util/IntervalList/IntervalListScatterMode.java @@ -75,6 +75,16 @@ public enum IntervalListScatterMode implements CommandLineParser.ClpEnum { * rather than the base level, for example CNV calling. */ INTERVAL_COUNT(IntervalListScattererByIntervalCount::new, "Scatter the interval list into similarly sized interval lists " + + "(by interval count, not by base count). " + + "Resulting interval lists will contain the same number of intervals except for the last, which contains the remainder."), + + /*** + * A scatter by interval **count** which attempts to fill each resulting interval list with approximately equal numbers + * of intervals, disregarding the base count. This approach distributes the remainder intervals across the initial interval lists. + * This is the preferred mode for whole genome joint calling and other scenarios where the interval list to be split + * contains a large number of intervals that should be distributed equally by count. + */ + INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER(IntervalListScattererByIntervalCountWithDistributedRemainder::new, "Scatter the interval list into similarly sized interval lists " + "(by interval count, not by base count). " + "Resulting interval lists will contain similar number of intervals."); diff --git a/src/main/java/picard/util/IntervalList/IntervalListScattererByIntervalCountWithDistributedRemainder.java b/src/main/java/picard/util/IntervalList/IntervalListScattererByIntervalCountWithDistributedRemainder.java new file mode 100644 index 0000000000..309b1a96ba --- /dev/null +++ b/src/main/java/picard/util/IntervalList/IntervalListScattererByIntervalCountWithDistributedRemainder.java @@ -0,0 +1,23 @@ +package picard.util.IntervalList; + +import htsjdk.samtools.util.Interval; +import htsjdk.samtools.util.IntervalList; + +import java.util.Arrays; +import java.util.List; + +/** + * Scatters {@link IntervalList} by into `interval count` shards so that resulting {@link IntervalList}'s have + * approximately same number of intervals in them. The "remainder" intervals are distributed over the last lists. + */ +public class IntervalListScattererByIntervalCountWithDistributedRemainder extends IntervalListScattererByIntervalCount { + + @Override + public List takeSome(final Interval interval, final long idealSplitWeight, final long currentSize, final double projectSizeOfRemaining) { + if (projectSizeOfRemaining > currentSize) { + return Arrays.asList(interval, null); + } else { + return Arrays.asList(null, interval); + } + } +} diff --git a/src/main/java/picard/util/IntervalListTools.java b/src/main/java/picard/util/IntervalListTools.java index a2e63e7ac3..ae682f3f20 100644 --- a/src/main/java/picard/util/IntervalListTools.java +++ b/src/main/java/picard/util/IntervalListTools.java @@ -455,7 +455,7 @@ protected int doWork() { if (SCATTER_CONTENT != null) { final long listSize = SUBDIVISION_MODE.make().listWeight(output); - SCATTER_COUNT = (int) listSize / SCATTER_CONTENT; + SCATTER_COUNT = (int)Math.round((double) listSize / SCATTER_CONTENT); LOG.info(String.format("Using SCATTER_CONTENT = %d and an interval of size %d, attempting to scatter into %s intervals.", SCATTER_CONTENT, listSize, SCATTER_COUNT)); } diff --git a/src/test/java/picard/util/IntervalListScattererTest.java b/src/test/java/picard/util/IntervalListScattererTest.java index 7477a8ef56..92a1bf521e 100644 --- a/src/test/java/picard/util/IntervalListScattererTest.java +++ b/src/test/java/picard/util/IntervalListScattererTest.java @@ -33,6 +33,7 @@ import java.io.File; import java.util.*; +import java.util.stream.Collectors; /** * Basic test for scatter functionality in IntervalListTools @@ -43,6 +44,12 @@ public class IntervalListScattererTest { private static final File INTERVAL_FILE = new File(TEST_DATA_DIR, "scatterable.interval_list"); private static final IntervalList LIST_TO_SCATTER = IntervalList.fromFile(INTERVAL_FILE); + static final File LARGER_INTERVAL_FILE = new File(TEST_DATA_DIR, "test.hg38.200.interval_list"); + private static final List LARGER_INTERVAL_EXPECTEDS = Arrays.asList(new File(TEST_DATA_DIR, "largeScatters").listFiles()); + static final List LARGER_EXPECTED_LISTS = LARGER_INTERVAL_EXPECTEDS.stream().sorted().flatMap(l -> Arrays.asList(l.listFiles()).stream().map(f -> IntervalList.fromFile(f))).collect(Collectors.toList()); + private static final List LARGER_INTERVAL_NO_REMAINDER_EXPECTEDS = Arrays.asList(new File(TEST_DATA_DIR, "largeScattersNoRemainder").listFiles()); + static final List LARGER_NO_REMAINDER_EXPECTED_LISTS = LARGER_INTERVAL_NO_REMAINDER_EXPECTEDS.stream().sorted().flatMap(l -> Arrays.asList(l.listFiles()).stream().map(f -> IntervalList.fromFile(f))).collect(Collectors.toList()); + private static final File INTERVAL_WITH_OVERFLOW_FILE = new File(TEST_DATA_DIR, "scatterable_with_overflow.interval_list"); private static final IntervalList LIST_TO_SCATTER_WITH_OVERFLOW = IntervalList.fromFile(INTERVAL_WITH_OVERFLOW_FILE); @@ -64,7 +71,7 @@ public String toString() { '}'; } - private Testcase(final File file, final int scatterWidth, final IntervalListScatterMode mode, final List expectedScatter) { + Testcase(final File file, final int scatterWidth, final IntervalListScatterMode mode, final List expectedScatter) { this.source = IntervalList.fromFile(file); this.file = file; this.expectedScatter = expectedScatter; @@ -73,8 +80,32 @@ private Testcase(final File file, final int scatterWidth, final IntervalListScat } } - @DataProvider - public static Iterator testScatterTestcases() { + /** + * These are split out separately and private because the treatment of remainders causes different behavior whether + * scatter count is specified (as similated here) versus whether scatter *content* is specified, as in in the IntervalListTools + * integration tests + * @return test cases with expected behavior for distributed remainder mode given a specified number of output lists + */ + private static List getRemainderTestcases() { + final List testCases = new ArrayList<>(); + testCases.add(new Testcase( + LARGER_INTERVAL_FILE, 60, IntervalListScatterMode.INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER, + LARGER_EXPECTED_LISTS + )); + + testCases.add(new Testcase( + LARGER_INTERVAL_FILE, 20, IntervalListScatterMode.INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER, + LARGER_NO_REMAINDER_EXPECTED_LISTS + )); + return testCases; + } + + /** + * These test cases for modes not including INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER have the same behavior + * + * @return + */ + public static List getScatterTestcases() { final List testCases = new ArrayList<>(); Assert.assertEquals(LIST_TO_SCATTER.getUniqueBaseCount(), 200, "Wrong unique base count"); Assert.assertEquals(LIST_TO_SCATTER_MANY.getUniqueBaseCount(), 32 * 2, "Wrong unique base count"); @@ -393,7 +424,14 @@ public static Iterator testScatterTestcases() { IntervalList.overlaps(LIST_TO_SCATTER_MANY, secondThird)) )))))); - return testCases.stream().map(tc -> new Object[]{tc}).iterator(); + return testCases; + } + + @DataProvider + public static Iterator testScatterTestcases() { + final List testcases = new ArrayList<>(getScatterTestcases()); + testcases.addAll(getRemainderTestcases()); + return testcases.stream().map(tc -> new Object[]{tc}).iterator(); } @Test(dataProvider = "testScatterTestcases") diff --git a/src/test/java/picard/util/IntervalListToolsTest.java b/src/test/java/picard/util/IntervalListToolsTest.java index 258a0bec90..1a4f5421fb 100644 --- a/src/test/java/picard/util/IntervalListToolsTest.java +++ b/src/test/java/picard/util/IntervalListToolsTest.java @@ -30,6 +30,7 @@ import org.testng.annotations.DataProvider; import org.testng.annotations.Test; import picard.cmdline.CommandLineProgramTest; +import picard.util.IntervalList.IntervalListScatterMode; import picard.util.IntervalList.IntervalListScatterer; import java.io.File; @@ -40,6 +41,7 @@ import java.util.List; import java.util.Objects; import java.util.Scanner; +import java.util.stream.Collectors; import java.util.stream.Stream; /** @@ -47,7 +49,7 @@ */ public class IntervalListToolsTest extends CommandLineProgramTest { - private final File TEST_DATA_DIR = new File("testdata/picard/util/"); + private static final File TEST_DATA_DIR = new File("testdata/picard/util/"); private final File scatterable = new File(TEST_DATA_DIR, "scatterable.interval_list"); private final File scatterableStdin = new File(TEST_DATA_DIR, "scatterable_stdin"); private final File secondInput = new File(TEST_DATA_DIR, "secondInput.interval_list"); @@ -55,6 +57,9 @@ public class IntervalListToolsTest extends CommandLineProgramTest { private final File abutting = new File(TEST_DATA_DIR, "abutting.interval_list"); private final File abutting_combined = new File(TEST_DATA_DIR, "abutting_combined.interval_list"); private final File abutting_notcombined = new File(TEST_DATA_DIR, "abutting_notcombined.interval_list"); + private static final List LARGER_EXPECTED_WITH_REMAINDER_FILES = Arrays.asList(new File(TEST_DATA_DIR, "largeScattersWithRemainder").listFiles()); + private static final List LARGER_EXPECTED_WITH_REMAINDER_LISTS = LARGER_EXPECTED_WITH_REMAINDER_FILES.stream().sorted().flatMap(l -> Arrays.asList(l.listFiles()).stream().map(f -> IntervalList.fromFile(f))).collect(Collectors.toList()); + @Test public void testSecondInputValidation() { @@ -293,10 +298,32 @@ private long testerCountOutput(IntervalListTools.Action action, IntervalListTool return reader.nextLong(); } + /** + * These are split out separately and private because the treatment of remainders causes different behavior whether + * scatter count is specified (as similated here) versus whether scatter *content* is specified, as in in the IntervalListTools + * integration tests + * @return test cases with expected behavior for distributed remainder mode given a specified number of output lists + */ + private static List getRemainderTestcases() { + final List testCases = new ArrayList<>(); + testCases.add(new IntervalListScattererTest.Testcase( + IntervalListScattererTest.LARGER_INTERVAL_FILE, 67, IntervalListScatterMode.INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER, + LARGER_EXPECTED_WITH_REMAINDER_LISTS + )); + + testCases.add(new IntervalListScattererTest.Testcase( + IntervalListScattererTest.LARGER_INTERVAL_FILE, 20, IntervalListScatterMode.INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER, + IntervalListScattererTest.LARGER_NO_REMAINDER_EXPECTED_LISTS + )); + return testCases; + } + // test scatter with different kinds of balancing. @DataProvider public static Iterator testScatterTestcases() { - return IntervalListScattererTest.testScatterTestcases(); + final List testcases = new ArrayList<>(IntervalListScattererTest.getScatterTestcases()); + testcases.addAll(getRemainderTestcases()); + return testcases.stream().map(tc -> new Object[]{tc}).iterator(); } private final List dirsToDelete = new ArrayList<>(); @@ -381,7 +408,7 @@ public void testScatterByContent(final IntervalListScattererTest.Testcase tc) th args.add("OUTPUT=" + ilOutDir); } - args.add("SCATTER_CONTENT=" + tc.mode.make().listWeight(tc.source) / tc.expectedScatter.size()); + args.add("SCATTER_CONTENT=" + (int)Math.round((double)tc.mode.make().listWeight(tc.source) / tc.expectedScatter.size())); Assert.assertEquals(runPicardCommandLine(args), 0); diff --git a/testdata/picard/util/largeScatters/temp_0001_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0001_of_60/scattered.interval_list new file mode 100644 index 0000000000..bd4ed775c3 --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0001_of_60/scattered.interval_list @@ -0,0 +1,7 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 1 195878 + target_1 +chr1 195879 391754 + target_2 +chr1 391755 606302 + target_3 +chr1 606303 820848 + target_4 diff --git a/testdata/picard/util/largeScatters/temp_0002_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0002_of_60/scattered.interval_list new file mode 100644 index 0000000000..cc3ec4452d --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0002_of_60/scattered.interval_list @@ -0,0 +1,7 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 820849 910849 + target_5 +chr1 910850 1000848 + target_6 +chr1 1000849 1112599 + target_7 +chr1 1112600 1224349 + target_8 diff --git a/testdata/picard/util/largeScatters/temp_0003_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0003_of_60/scattered.interval_list new file mode 100644 index 0000000000..c6a018aba9 --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0003_of_60/scattered.interval_list @@ -0,0 +1,7 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 1224350 1348642 + target_9 +chr1 1348643 1472934 + target_10 +chr1 1472935 1584197 + target_11 +chr1 1584198 1695459 + target_12 diff --git a/testdata/picard/util/largeScatters/temp_0004_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0004_of_60/scattered.interval_list new file mode 100644 index 0000000000..4339f63bb6 --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0004_of_60/scattered.interval_list @@ -0,0 +1,7 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 1695460 1815724 + target_13 +chr1 1815725 1935987 + target_14 +chr1 1935988 2030188 + target_15 +chr1 2030189 2124387 + target_16 diff --git a/testdata/picard/util/largeScatters/temp_0005_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0005_of_60/scattered.interval_list new file mode 100644 index 0000000000..75f23f053b --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0005_of_60/scattered.interval_list @@ -0,0 +1,7 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 2124388 2261379 + target_17 +chr1 2261380 2398369 + target_18 +chr1 2398370 2662724 + target_19 +chr1 2662725 2927077 + target_20 diff --git a/testdata/picard/util/largeScatters/temp_0006_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0006_of_60/scattered.interval_list new file mode 100644 index 0000000000..a19ecccdd1 --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0006_of_60/scattered.interval_list @@ -0,0 +1,7 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 2927078 3044965 + target_21 +chr1 3044966 3162852 + target_22 +chr1 3162853 3261512 + target_23 +chr1 3261513 3360170 + target_24 diff --git a/testdata/picard/util/largeScatters/temp_0007_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0007_of_60/scattered.interval_list new file mode 100644 index 0000000000..4984d4998e --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0007_of_60/scattered.interval_list @@ -0,0 +1,7 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 3360171 3481821 + target_25 +chr1 3481822 3603470 + target_26 +chr1 3603471 3720976 + target_27 +chr1 3720977 3838480 + target_28 diff --git a/testdata/picard/util/largeScatters/temp_0008_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0008_of_60/scattered.interval_list new file mode 100644 index 0000000000..0f480de378 --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0008_of_60/scattered.interval_list @@ -0,0 +1,7 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 3838481 3931034 + target_29 +chr1 3931035 4023586 + target_30 +chr1 4023587 4132844 + target_31 +chr1 4132845 4242101 + target_32 diff --git a/testdata/picard/util/largeScatters/temp_0009_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0009_of_60/scattered.interval_list new file mode 100644 index 0000000000..b9e6b3f1c8 --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0009_of_60/scattered.interval_list @@ -0,0 +1,7 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 4242102 4345574 + target_33 +chr1 4345575 4449046 + target_34 +chr1 4449047 4543247 + target_35 +chr1 4543248 4637446 + target_36 diff --git a/testdata/picard/util/largeScatters/temp_0010_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0010_of_60/scattered.interval_list new file mode 100644 index 0000000000..4bf0dc0562 --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0010_of_60/scattered.interval_list @@ -0,0 +1,7 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 4637447 4761514 + target_37 +chr1 4761515 4885581 + target_38 +chr1 4885582 5011314 + target_39 +chr1 5011315 5137046 + target_40 diff --git a/testdata/picard/util/largeScatters/temp_0011_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0011_of_60/scattered.interval_list new file mode 100644 index 0000000000..5fbb39ebc3 --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0011_of_60/scattered.interval_list @@ -0,0 +1,7 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 5137047 5243668 + target_41 +chr1 5243669 5350289 + target_42 +chr1 5350290 5485729 + target_43 +chr1 5485730 5621168 + target_44 diff --git a/testdata/picard/util/largeScatters/temp_0012_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0012_of_60/scattered.interval_list new file mode 100644 index 0000000000..dd15c9c896 --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0012_of_60/scattered.interval_list @@ -0,0 +1,7 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 5621169 5745096 + target_45 +chr1 5745097 5869022 + target_46 +chr1 5869023 6009743 + target_47 +chr1 6009744 6150463 + target_48 diff --git a/testdata/picard/util/largeScatters/temp_0013_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0013_of_60/scattered.interval_list new file mode 100644 index 0000000000..a42d89237d --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0013_of_60/scattered.interval_list @@ -0,0 +1,7 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 6150464 6288718 + target_49 +chr1 6288719 6426971 + target_50 +chr1 6426972 6569464 + target_51 +chr1 6569465 6711955 + target_52 diff --git a/testdata/picard/util/largeScatters/temp_0014_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0014_of_60/scattered.interval_list new file mode 100644 index 0000000000..b3bd4cd608 --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0014_of_60/scattered.interval_list @@ -0,0 +1,7 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 6711956 6864915 + target_53 +chr1 6864916 7017874 + target_54 +chr1 7017875 7160373 + target_55 +chr1 7160374 7302870 + target_56 diff --git a/testdata/picard/util/largeScatters/temp_0015_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0015_of_60/scattered.interval_list new file mode 100644 index 0000000000..1021688ded --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0015_of_60/scattered.interval_list @@ -0,0 +1,7 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 7302871 7411540 + target_57 +chr1 7411541 7520208 + target_58 +chr1 7520209 7670001 + target_59 +chr1 7670002 7819792 + target_60 diff --git a/testdata/picard/util/largeScatters/temp_0016_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0016_of_60/scattered.interval_list new file mode 100644 index 0000000000..b15b9447d0 --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0016_of_60/scattered.interval_list @@ -0,0 +1,7 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 7819793 7955554 + target_61 +chr1 7955555 8091315 + target_62 +chr1 8091316 8192379 + target_63 +chr1 8192380 8293442 + target_64 diff --git a/testdata/picard/util/largeScatters/temp_0017_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0017_of_60/scattered.interval_list new file mode 100644 index 0000000000..56291d4b3f --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0017_of_60/scattered.interval_list @@ -0,0 +1,7 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 8293443 8451663 + target_65 +chr1 8451664 8609883 + target_66 +chr1 8609884 8776005 + target_67 +chr1 8776006 8942125 + target_68 diff --git a/testdata/picard/util/largeScatters/temp_0018_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0018_of_60/scattered.interval_list new file mode 100644 index 0000000000..4bddfc69ef --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0018_of_60/scattered.interval_list @@ -0,0 +1,7 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 8942126 9066968 + target_69 +chr1 9066969 9191810 + target_70 +chr1 9191811 9290757 + target_71 +chr1 9290758 9389703 + target_72 diff --git a/testdata/picard/util/largeScatters/temp_0019_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0019_of_60/scattered.interval_list new file mode 100644 index 0000000000..9e0276d9e5 --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0019_of_60/scattered.interval_list @@ -0,0 +1,7 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 9389704 9530072 + target_73 +chr1 9530073 9670439 + target_74 +chr1 9670440 9851576 + target_75 +chr1 9851577 10032712 + target_76 diff --git a/testdata/picard/util/largeScatters/temp_0020_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0020_of_60/scattered.interval_list new file mode 100644 index 0000000000..2fc3a16aaa --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0020_of_60/scattered.interval_list @@ -0,0 +1,7 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 10032713 10183181 + target_77 +chr1 10183182 10333649 + target_78 +chr1 10333650 10457488 + target_79 +chr1 10457489 10581325 + target_80 diff --git a/testdata/picard/util/largeScatters/temp_0021_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0021_of_60/scattered.interval_list new file mode 100644 index 0000000000..9c20e8a739 --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0021_of_60/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 10581326 10749793 + target_81 +chr1 10749794 10918259 + target_82 +chr1 10918260 11027532 + target_83 diff --git a/testdata/picard/util/largeScatters/temp_0022_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0022_of_60/scattered.interval_list new file mode 100644 index 0000000000..d4cdf26bf5 --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0022_of_60/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 11027533 11136803 + target_84 +chr1 11136804 11280317 + target_85 +chr1 11280318 11423830 + target_86 diff --git a/testdata/picard/util/largeScatters/temp_0023_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0023_of_60/scattered.interval_list new file mode 100644 index 0000000000..75f73dc7c1 --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0023_of_60/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 11423831 11549522 + target_87 +chr1 11549523 11675212 + target_88 +chr1 11675213 11776165 + target_89 diff --git a/testdata/picard/util/largeScatters/temp_0024_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0024_of_60/scattered.interval_list new file mode 100644 index 0000000000..c6ff2efae8 --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0024_of_60/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 11776166 11877116 + target_90 +chr1 11877117 12000862 + target_91 +chr1 12000863 12124606 + target_92 diff --git a/testdata/picard/util/largeScatters/temp_0025_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0025_of_60/scattered.interval_list new file mode 100644 index 0000000000..a49f330da4 --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0025_of_60/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 12124607 12343496 + target_93 +chr1 12343497 12562384 + target_94 +chr1 12562385 12694554 + target_95 diff --git a/testdata/picard/util/largeScatters/temp_0026_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0026_of_60/scattered.interval_list new file mode 100644 index 0000000000..255bdb8175 --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0026_of_60/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 12694555 12826723 + target_96 +chr1 12826724 13005745 + target_97 +chr1 13005746 13184766 + target_98 diff --git a/testdata/picard/util/largeScatters/temp_0027_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0027_of_60/scattered.interval_list new file mode 100644 index 0000000000..63c6c78adc --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0027_of_60/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 13184767 13327643 + target_99 +chr1 13327644 13470518 + target_100 +chr1 13470519 13566626 + target_101 diff --git a/testdata/picard/util/largeScatters/temp_0028_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0028_of_60/scattered.interval_list new file mode 100644 index 0000000000..662742d6ff --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0028_of_60/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 13566627 13662732 + target_102 +chr1 13662733 13806001 + target_103 +chr1 13806002 13949268 + target_104 diff --git a/testdata/picard/util/largeScatters/temp_0029_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0029_of_60/scattered.interval_list new file mode 100644 index 0000000000..d873d70581 --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0029_of_60/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 13949269 14043588 + target_105 +chr1 14043589 14137907 + target_106 +chr1 14137908 14272203 + target_107 diff --git a/testdata/picard/util/largeScatters/temp_0030_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0030_of_60/scattered.interval_list new file mode 100644 index 0000000000..5929774f59 --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0030_of_60/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 14272204 14406498 + target_108 +chr1 14406499 14551515 + target_109 +chr1 14551516 14696530 + target_110 diff --git a/testdata/picard/util/largeScatters/temp_0031_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0031_of_60/scattered.interval_list new file mode 100644 index 0000000000..c13f23813b --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0031_of_60/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 14696531 14813755 + target_111 +chr1 14813756 14930979 + target_112 +chr1 14930980 15035314 + target_113 diff --git a/testdata/picard/util/largeScatters/temp_0032_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0032_of_60/scattered.interval_list new file mode 100644 index 0000000000..da6dc0c510 --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0032_of_60/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 15035315 15139648 + target_114 +chr1 15139649 15237194 + target_115 +chr1 15237195 15334738 + target_116 diff --git a/testdata/picard/util/largeScatters/temp_0033_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0033_of_60/scattered.interval_list new file mode 100644 index 0000000000..daa8bf5b24 --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0033_of_60/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 15334739 15458284 + target_117 +chr1 15458285 15581828 + target_118 +chr1 15581829 15703637 + target_119 diff --git a/testdata/picard/util/largeScatters/temp_0034_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0034_of_60/scattered.interval_list new file mode 100644 index 0000000000..6c65c1734a --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0034_of_60/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 15703638 15825445 + target_120 +chr1 15825446 15939965 + target_121 +chr1 15939966 16054483 + target_122 diff --git a/testdata/picard/util/largeScatters/temp_0035_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0035_of_60/scattered.interval_list new file mode 100644 index 0000000000..f1a00a082e --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0035_of_60/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 16054484 16171468 + target_123 +chr1 16171469 16288452 + target_124 +chr1 16288453 16398909 + target_125 diff --git a/testdata/picard/util/largeScatters/temp_0036_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0036_of_60/scattered.interval_list new file mode 100644 index 0000000000..0d36881193 --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0036_of_60/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 16398910 16509364 + target_126 +chr1 16509365 16549703 + target_127 +chr1 16549704 16590041 + target_128 diff --git a/testdata/picard/util/largeScatters/temp_0037_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0037_of_60/scattered.interval_list new file mode 100644 index 0000000000..7be2e4f654 --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0037_of_60/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 16590042 16638247 + target_129 +chr1 16638248 16686451 + target_130 +chr1 16686452 16742020 + target_131 diff --git a/testdata/picard/util/largeScatters/temp_0038_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0038_of_60/scattered.interval_list new file mode 100644 index 0000000000..1cc262c852 --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0038_of_60/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 16742021 16797588 + target_132 +chr1 16797589 16883908 + target_133 +chr1 16883909 16970227 + target_134 diff --git a/testdata/picard/util/largeScatters/temp_0039_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0039_of_60/scattered.interval_list new file mode 100644 index 0000000000..48ea5f30ef --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0039_of_60/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 16970228 17089415 + target_135 +chr1 17089416 17208601 + target_136 +chr1 17208602 17303634 + target_137 diff --git a/testdata/picard/util/largeScatters/temp_0040_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0040_of_60/scattered.interval_list new file mode 100644 index 0000000000..248ec795a1 --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0040_of_60/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 17303635 17398666 + target_138 +chr1 17398667 17535915 + target_139 +chr1 17535916 17673163 + target_140 diff --git a/testdata/picard/util/largeScatters/temp_0041_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0041_of_60/scattered.interval_list new file mode 100644 index 0000000000..afb17ad83c --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0041_of_60/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 17673164 17803647 + target_141 +chr1 17803648 17934130 + target_142 +chr1 17934131 18055738 + target_143 diff --git a/testdata/picard/util/largeScatters/temp_0042_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0042_of_60/scattered.interval_list new file mode 100644 index 0000000000..ba77fb6792 --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0042_of_60/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 18055739 18177344 + target_144 +chr1 18177345 18305108 + target_145 +chr1 18305109 18432871 + target_146 diff --git a/testdata/picard/util/largeScatters/temp_0043_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0043_of_60/scattered.interval_list new file mode 100644 index 0000000000..4fc204f033 --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0043_of_60/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 18432872 18559883 + target_147 +chr1 18559884 18686893 + target_148 +chr1 18686894 18797287 + target_149 diff --git a/testdata/picard/util/largeScatters/temp_0044_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0044_of_60/scattered.interval_list new file mode 100644 index 0000000000..544be8eda8 --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0044_of_60/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 18797288 18907680 + target_150 +chr1 18907681 19040869 + target_151 +chr1 19040870 19174057 + target_152 diff --git a/testdata/picard/util/largeScatters/temp_0045_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0045_of_60/scattered.interval_list new file mode 100644 index 0000000000..358f09e9aa --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0045_of_60/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 19174058 19300251 + target_153 +chr1 19300252 19426443 + target_154 +chr1 19426444 19524828 + target_155 diff --git a/testdata/picard/util/largeScatters/temp_0046_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0046_of_60/scattered.interval_list new file mode 100644 index 0000000000..47daa63a28 --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0046_of_60/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 19524829 19623211 + target_156 +chr1 19623212 19743520 + target_157 +chr1 19743521 19863828 + target_158 diff --git a/testdata/picard/util/largeScatters/temp_0047_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0047_of_60/scattered.interval_list new file mode 100644 index 0000000000..378253010f --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0047_of_60/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 19863829 20021799 + target_159 +chr1 20021800 20179768 + target_160 +chr1 20179769 20319195 + target_161 diff --git a/testdata/picard/util/largeScatters/temp_0048_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0048_of_60/scattered.interval_list new file mode 100644 index 0000000000..271dd2416f --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0048_of_60/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 20319196 20458621 + target_162 +chr1 20458622 20576129 + target_163 +chr1 20576130 20693635 + target_164 diff --git a/testdata/picard/util/largeScatters/temp_0049_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0049_of_60/scattered.interval_list new file mode 100644 index 0000000000..2052c90135 --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0049_of_60/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 20693636 20871153 + target_165 +chr1 20871154 21048670 + target_166 +chr1 21048671 21206463 + target_167 diff --git a/testdata/picard/util/largeScatters/temp_0050_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0050_of_60/scattered.interval_list new file mode 100644 index 0000000000..46ffbe4fb1 --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0050_of_60/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 21206464 21364254 + target_168 +chr1 21364255 21466916 + target_169 +chr1 21466917 21569576 + target_170 diff --git a/testdata/picard/util/largeScatters/temp_0051_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0051_of_60/scattered.interval_list new file mode 100644 index 0000000000..24793d0ae5 --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0051_of_60/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 21569577 21693920 + target_171 +chr1 21693921 21818263 + target_172 +chr1 21818264 21912191 + target_173 diff --git a/testdata/picard/util/largeScatters/temp_0052_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0052_of_60/scattered.interval_list new file mode 100644 index 0000000000..a666ce047d --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0052_of_60/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 21912192 22006117 + target_174 +chr1 22006118 22110817 + target_175 +chr1 22110818 22215516 + target_176 diff --git a/testdata/picard/util/largeScatters/temp_0053_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0053_of_60/scattered.interval_list new file mode 100644 index 0000000000..3a2bc58a0b --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0053_of_60/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 22215517 22340628 + target_177 +chr1 22340629 22465738 + target_178 +chr1 22465739 22607396 + target_179 diff --git a/testdata/picard/util/largeScatters/temp_0054_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0054_of_60/scattered.interval_list new file mode 100644 index 0000000000..73cb8fc739 --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0054_of_60/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 22607397 22749052 + target_180 +chr1 22749053 22906130 + target_181 +chr1 22906131 23063207 + target_182 diff --git a/testdata/picard/util/largeScatters/temp_0055_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0055_of_60/scattered.interval_list new file mode 100644 index 0000000000..cf86e4bcae --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0055_of_60/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 23063208 23237804 + target_183 +chr1 23237805 23412399 + target_184 +chr1 23412400 23568271 + target_185 diff --git a/testdata/picard/util/largeScatters/temp_0056_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0056_of_60/scattered.interval_list new file mode 100644 index 0000000000..e584ae806a --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0056_of_60/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 23568272 23724141 + target_186 +chr1 23724142 23849296 + target_187 +chr1 23849297 23974450 + target_188 diff --git a/testdata/picard/util/largeScatters/temp_0057_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0057_of_60/scattered.interval_list new file mode 100644 index 0000000000..c1d7e83d86 --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0057_of_60/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 23974451 24070586 + target_189 +chr1 24070587 24166720 + target_190 +chr1 24166721 24294271 + target_191 diff --git a/testdata/picard/util/largeScatters/temp_0058_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0058_of_60/scattered.interval_list new file mode 100644 index 0000000000..c2e924fdd9 --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0058_of_60/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 24294272 24421820 + target_192 +chr1 24421821 24543637 + target_193 +chr1 24543638 24665452 + target_194 diff --git a/testdata/picard/util/largeScatters/temp_0059_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0059_of_60/scattered.interval_list new file mode 100644 index 0000000000..219a4aa37e --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0059_of_60/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 24665453 24822768 + target_195 +chr1 24822769 24980083 + target_196 +chr1 24980084 25097392 + target_197 diff --git a/testdata/picard/util/largeScatters/temp_0060_of_60/scattered.interval_list b/testdata/picard/util/largeScatters/temp_0060_of_60/scattered.interval_list new file mode 100644 index 0000000000..e36c74ea4e --- /dev/null +++ b/testdata/picard/util/largeScatters/temp_0060_of_60/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScatters --SCATTER_COUNT 60 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 25097393 25214699 + target_198 +chr1 25214700 25374885 + target_199 +chr1 25374886 25535069 + target_200 diff --git a/testdata/picard/util/largeScattersNoRemainder/temp_0001_of_20/scattered.interval_list b/testdata/picard/util/largeScattersNoRemainder/temp_0001_of_20/scattered.interval_list new file mode 100644 index 0000000000..1e2fee5728 --- /dev/null +++ b/testdata/picard/util/largeScattersNoRemainder/temp_0001_of_20/scattered.interval_list @@ -0,0 +1,13 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersNoRemainder --SCATTER_COUNT 20 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 1 195878 + target_1 +chr1 195879 391754 + target_2 +chr1 391755 606302 + target_3 +chr1 606303 820848 + target_4 +chr1 820849 910849 + target_5 +chr1 910850 1000848 + target_6 +chr1 1000849 1112599 + target_7 +chr1 1112600 1224349 + target_8 +chr1 1224350 1348642 + target_9 +chr1 1348643 1472934 + target_10 diff --git a/testdata/picard/util/largeScattersNoRemainder/temp_0002_of_20/scattered.interval_list b/testdata/picard/util/largeScattersNoRemainder/temp_0002_of_20/scattered.interval_list new file mode 100644 index 0000000000..0c74206e5b --- /dev/null +++ b/testdata/picard/util/largeScattersNoRemainder/temp_0002_of_20/scattered.interval_list @@ -0,0 +1,13 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersNoRemainder --SCATTER_COUNT 20 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 1472935 1584197 + target_11 +chr1 1584198 1695459 + target_12 +chr1 1695460 1815724 + target_13 +chr1 1815725 1935987 + target_14 +chr1 1935988 2030188 + target_15 +chr1 2030189 2124387 + target_16 +chr1 2124388 2261379 + target_17 +chr1 2261380 2398369 + target_18 +chr1 2398370 2662724 + target_19 +chr1 2662725 2927077 + target_20 diff --git a/testdata/picard/util/largeScattersNoRemainder/temp_0003_of_20/scattered.interval_list b/testdata/picard/util/largeScattersNoRemainder/temp_0003_of_20/scattered.interval_list new file mode 100644 index 0000000000..5b4372ee59 --- /dev/null +++ b/testdata/picard/util/largeScattersNoRemainder/temp_0003_of_20/scattered.interval_list @@ -0,0 +1,13 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersNoRemainder --SCATTER_COUNT 20 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 2927078 3044965 + target_21 +chr1 3044966 3162852 + target_22 +chr1 3162853 3261512 + target_23 +chr1 3261513 3360170 + target_24 +chr1 3360171 3481821 + target_25 +chr1 3481822 3603470 + target_26 +chr1 3603471 3720976 + target_27 +chr1 3720977 3838480 + target_28 +chr1 3838481 3931034 + target_29 +chr1 3931035 4023586 + target_30 diff --git a/testdata/picard/util/largeScattersNoRemainder/temp_0004_of_20/scattered.interval_list b/testdata/picard/util/largeScattersNoRemainder/temp_0004_of_20/scattered.interval_list new file mode 100644 index 0000000000..079c717886 --- /dev/null +++ b/testdata/picard/util/largeScattersNoRemainder/temp_0004_of_20/scattered.interval_list @@ -0,0 +1,13 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersNoRemainder --SCATTER_COUNT 20 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 4023587 4132844 + target_31 +chr1 4132845 4242101 + target_32 +chr1 4242102 4345574 + target_33 +chr1 4345575 4449046 + target_34 +chr1 4449047 4543247 + target_35 +chr1 4543248 4637446 + target_36 +chr1 4637447 4761514 + target_37 +chr1 4761515 4885581 + target_38 +chr1 4885582 5011314 + target_39 +chr1 5011315 5137046 + target_40 diff --git a/testdata/picard/util/largeScattersNoRemainder/temp_0005_of_20/scattered.interval_list b/testdata/picard/util/largeScattersNoRemainder/temp_0005_of_20/scattered.interval_list new file mode 100644 index 0000000000..ef91a20042 --- /dev/null +++ b/testdata/picard/util/largeScattersNoRemainder/temp_0005_of_20/scattered.interval_list @@ -0,0 +1,13 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersNoRemainder --SCATTER_COUNT 20 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 5137047 5243668 + target_41 +chr1 5243669 5350289 + target_42 +chr1 5350290 5485729 + target_43 +chr1 5485730 5621168 + target_44 +chr1 5621169 5745096 + target_45 +chr1 5745097 5869022 + target_46 +chr1 5869023 6009743 + target_47 +chr1 6009744 6150463 + target_48 +chr1 6150464 6288718 + target_49 +chr1 6288719 6426971 + target_50 diff --git a/testdata/picard/util/largeScattersNoRemainder/temp_0006_of_20/scattered.interval_list b/testdata/picard/util/largeScattersNoRemainder/temp_0006_of_20/scattered.interval_list new file mode 100644 index 0000000000..2520efa605 --- /dev/null +++ b/testdata/picard/util/largeScattersNoRemainder/temp_0006_of_20/scattered.interval_list @@ -0,0 +1,13 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersNoRemainder --SCATTER_COUNT 20 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 6426972 6569464 + target_51 +chr1 6569465 6711955 + target_52 +chr1 6711956 6864915 + target_53 +chr1 6864916 7017874 + target_54 +chr1 7017875 7160373 + target_55 +chr1 7160374 7302870 + target_56 +chr1 7302871 7411540 + target_57 +chr1 7411541 7520208 + target_58 +chr1 7520209 7670001 + target_59 +chr1 7670002 7819792 + target_60 diff --git a/testdata/picard/util/largeScattersNoRemainder/temp_0007_of_20/scattered.interval_list b/testdata/picard/util/largeScattersNoRemainder/temp_0007_of_20/scattered.interval_list new file mode 100644 index 0000000000..521fdeb201 --- /dev/null +++ b/testdata/picard/util/largeScattersNoRemainder/temp_0007_of_20/scattered.interval_list @@ -0,0 +1,13 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersNoRemainder --SCATTER_COUNT 20 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 7819793 7955554 + target_61 +chr1 7955555 8091315 + target_62 +chr1 8091316 8192379 + target_63 +chr1 8192380 8293442 + target_64 +chr1 8293443 8451663 + target_65 +chr1 8451664 8609883 + target_66 +chr1 8609884 8776005 + target_67 +chr1 8776006 8942125 + target_68 +chr1 8942126 9066968 + target_69 +chr1 9066969 9191810 + target_70 diff --git a/testdata/picard/util/largeScattersNoRemainder/temp_0008_of_20/scattered.interval_list b/testdata/picard/util/largeScattersNoRemainder/temp_0008_of_20/scattered.interval_list new file mode 100644 index 0000000000..ee592a77ec --- /dev/null +++ b/testdata/picard/util/largeScattersNoRemainder/temp_0008_of_20/scattered.interval_list @@ -0,0 +1,13 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersNoRemainder --SCATTER_COUNT 20 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 9191811 9290757 + target_71 +chr1 9290758 9389703 + target_72 +chr1 9389704 9530072 + target_73 +chr1 9530073 9670439 + target_74 +chr1 9670440 9851576 + target_75 +chr1 9851577 10032712 + target_76 +chr1 10032713 10183181 + target_77 +chr1 10183182 10333649 + target_78 +chr1 10333650 10457488 + target_79 +chr1 10457489 10581325 + target_80 diff --git a/testdata/picard/util/largeScattersNoRemainder/temp_0009_of_20/scattered.interval_list b/testdata/picard/util/largeScattersNoRemainder/temp_0009_of_20/scattered.interval_list new file mode 100644 index 0000000000..60a5bd5af7 --- /dev/null +++ b/testdata/picard/util/largeScattersNoRemainder/temp_0009_of_20/scattered.interval_list @@ -0,0 +1,13 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersNoRemainder --SCATTER_COUNT 20 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 10581326 10749793 + target_81 +chr1 10749794 10918259 + target_82 +chr1 10918260 11027532 + target_83 +chr1 11027533 11136803 + target_84 +chr1 11136804 11280317 + target_85 +chr1 11280318 11423830 + target_86 +chr1 11423831 11549522 + target_87 +chr1 11549523 11675212 + target_88 +chr1 11675213 11776165 + target_89 +chr1 11776166 11877116 + target_90 diff --git a/testdata/picard/util/largeScattersNoRemainder/temp_0010_of_20/scattered.interval_list b/testdata/picard/util/largeScattersNoRemainder/temp_0010_of_20/scattered.interval_list new file mode 100644 index 0000000000..54fd355b6b --- /dev/null +++ b/testdata/picard/util/largeScattersNoRemainder/temp_0010_of_20/scattered.interval_list @@ -0,0 +1,13 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersNoRemainder --SCATTER_COUNT 20 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 11877117 12000862 + target_91 +chr1 12000863 12124606 + target_92 +chr1 12124607 12343496 + target_93 +chr1 12343497 12562384 + target_94 +chr1 12562385 12694554 + target_95 +chr1 12694555 12826723 + target_96 +chr1 12826724 13005745 + target_97 +chr1 13005746 13184766 + target_98 +chr1 13184767 13327643 + target_99 +chr1 13327644 13470518 + target_100 diff --git a/testdata/picard/util/largeScattersNoRemainder/temp_0011_of_20/scattered.interval_list b/testdata/picard/util/largeScattersNoRemainder/temp_0011_of_20/scattered.interval_list new file mode 100644 index 0000000000..5c7af9131c --- /dev/null +++ b/testdata/picard/util/largeScattersNoRemainder/temp_0011_of_20/scattered.interval_list @@ -0,0 +1,13 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersNoRemainder --SCATTER_COUNT 20 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 13470519 13566626 + target_101 +chr1 13566627 13662732 + target_102 +chr1 13662733 13806001 + target_103 +chr1 13806002 13949268 + target_104 +chr1 13949269 14043588 + target_105 +chr1 14043589 14137907 + target_106 +chr1 14137908 14272203 + target_107 +chr1 14272204 14406498 + target_108 +chr1 14406499 14551515 + target_109 +chr1 14551516 14696530 + target_110 diff --git a/testdata/picard/util/largeScattersNoRemainder/temp_0012_of_20/scattered.interval_list b/testdata/picard/util/largeScattersNoRemainder/temp_0012_of_20/scattered.interval_list new file mode 100644 index 0000000000..ca65cef8ee --- /dev/null +++ b/testdata/picard/util/largeScattersNoRemainder/temp_0012_of_20/scattered.interval_list @@ -0,0 +1,13 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersNoRemainder --SCATTER_COUNT 20 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 14696531 14813755 + target_111 +chr1 14813756 14930979 + target_112 +chr1 14930980 15035314 + target_113 +chr1 15035315 15139648 + target_114 +chr1 15139649 15237194 + target_115 +chr1 15237195 15334738 + target_116 +chr1 15334739 15458284 + target_117 +chr1 15458285 15581828 + target_118 +chr1 15581829 15703637 + target_119 +chr1 15703638 15825445 + target_120 diff --git a/testdata/picard/util/largeScattersNoRemainder/temp_0013_of_20/scattered.interval_list b/testdata/picard/util/largeScattersNoRemainder/temp_0013_of_20/scattered.interval_list new file mode 100644 index 0000000000..3a0206109c --- /dev/null +++ b/testdata/picard/util/largeScattersNoRemainder/temp_0013_of_20/scattered.interval_list @@ -0,0 +1,13 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersNoRemainder --SCATTER_COUNT 20 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 15825446 15939965 + target_121 +chr1 15939966 16054483 + target_122 +chr1 16054484 16171468 + target_123 +chr1 16171469 16288452 + target_124 +chr1 16288453 16398909 + target_125 +chr1 16398910 16509364 + target_126 +chr1 16509365 16549703 + target_127 +chr1 16549704 16590041 + target_128 +chr1 16590042 16638247 + target_129 +chr1 16638248 16686451 + target_130 diff --git a/testdata/picard/util/largeScattersNoRemainder/temp_0014_of_20/scattered.interval_list b/testdata/picard/util/largeScattersNoRemainder/temp_0014_of_20/scattered.interval_list new file mode 100644 index 0000000000..93b7dffed7 --- /dev/null +++ b/testdata/picard/util/largeScattersNoRemainder/temp_0014_of_20/scattered.interval_list @@ -0,0 +1,13 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersNoRemainder --SCATTER_COUNT 20 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 16686452 16742020 + target_131 +chr1 16742021 16797588 + target_132 +chr1 16797589 16883908 + target_133 +chr1 16883909 16970227 + target_134 +chr1 16970228 17089415 + target_135 +chr1 17089416 17208601 + target_136 +chr1 17208602 17303634 + target_137 +chr1 17303635 17398666 + target_138 +chr1 17398667 17535915 + target_139 +chr1 17535916 17673163 + target_140 diff --git a/testdata/picard/util/largeScattersNoRemainder/temp_0015_of_20/scattered.interval_list b/testdata/picard/util/largeScattersNoRemainder/temp_0015_of_20/scattered.interval_list new file mode 100644 index 0000000000..a02f619f66 --- /dev/null +++ b/testdata/picard/util/largeScattersNoRemainder/temp_0015_of_20/scattered.interval_list @@ -0,0 +1,13 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersNoRemainder --SCATTER_COUNT 20 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 17673164 17803647 + target_141 +chr1 17803648 17934130 + target_142 +chr1 17934131 18055738 + target_143 +chr1 18055739 18177344 + target_144 +chr1 18177345 18305108 + target_145 +chr1 18305109 18432871 + target_146 +chr1 18432872 18559883 + target_147 +chr1 18559884 18686893 + target_148 +chr1 18686894 18797287 + target_149 +chr1 18797288 18907680 + target_150 diff --git a/testdata/picard/util/largeScattersNoRemainder/temp_0016_of_20/scattered.interval_list b/testdata/picard/util/largeScattersNoRemainder/temp_0016_of_20/scattered.interval_list new file mode 100644 index 0000000000..b51f2d23ed --- /dev/null +++ b/testdata/picard/util/largeScattersNoRemainder/temp_0016_of_20/scattered.interval_list @@ -0,0 +1,13 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersNoRemainder --SCATTER_COUNT 20 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 18907681 19040869 + target_151 +chr1 19040870 19174057 + target_152 +chr1 19174058 19300251 + target_153 +chr1 19300252 19426443 + target_154 +chr1 19426444 19524828 + target_155 +chr1 19524829 19623211 + target_156 +chr1 19623212 19743520 + target_157 +chr1 19743521 19863828 + target_158 +chr1 19863829 20021799 + target_159 +chr1 20021800 20179768 + target_160 diff --git a/testdata/picard/util/largeScattersNoRemainder/temp_0017_of_20/scattered.interval_list b/testdata/picard/util/largeScattersNoRemainder/temp_0017_of_20/scattered.interval_list new file mode 100644 index 0000000000..e346bc46f5 --- /dev/null +++ b/testdata/picard/util/largeScattersNoRemainder/temp_0017_of_20/scattered.interval_list @@ -0,0 +1,13 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersNoRemainder --SCATTER_COUNT 20 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 20179769 20319195 + target_161 +chr1 20319196 20458621 + target_162 +chr1 20458622 20576129 + target_163 +chr1 20576130 20693635 + target_164 +chr1 20693636 20871153 + target_165 +chr1 20871154 21048670 + target_166 +chr1 21048671 21206463 + target_167 +chr1 21206464 21364254 + target_168 +chr1 21364255 21466916 + target_169 +chr1 21466917 21569576 + target_170 diff --git a/testdata/picard/util/largeScattersNoRemainder/temp_0018_of_20/scattered.interval_list b/testdata/picard/util/largeScattersNoRemainder/temp_0018_of_20/scattered.interval_list new file mode 100644 index 0000000000..e330bc2cb7 --- /dev/null +++ b/testdata/picard/util/largeScattersNoRemainder/temp_0018_of_20/scattered.interval_list @@ -0,0 +1,13 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersNoRemainder --SCATTER_COUNT 20 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 21569577 21693920 + target_171 +chr1 21693921 21818263 + target_172 +chr1 21818264 21912191 + target_173 +chr1 21912192 22006117 + target_174 +chr1 22006118 22110817 + target_175 +chr1 22110818 22215516 + target_176 +chr1 22215517 22340628 + target_177 +chr1 22340629 22465738 + target_178 +chr1 22465739 22607396 + target_179 +chr1 22607397 22749052 + target_180 diff --git a/testdata/picard/util/largeScattersNoRemainder/temp_0019_of_20/scattered.interval_list b/testdata/picard/util/largeScattersNoRemainder/temp_0019_of_20/scattered.interval_list new file mode 100644 index 0000000000..9e5084c5cc --- /dev/null +++ b/testdata/picard/util/largeScattersNoRemainder/temp_0019_of_20/scattered.interval_list @@ -0,0 +1,13 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersNoRemainder --SCATTER_COUNT 20 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 22749053 22906130 + target_181 +chr1 22906131 23063207 + target_182 +chr1 23063208 23237804 + target_183 +chr1 23237805 23412399 + target_184 +chr1 23412400 23568271 + target_185 +chr1 23568272 23724141 + target_186 +chr1 23724142 23849296 + target_187 +chr1 23849297 23974450 + target_188 +chr1 23974451 24070586 + target_189 +chr1 24070587 24166720 + target_190 diff --git a/testdata/picard/util/largeScattersNoRemainder/temp_0020_of_20/scattered.interval_list b/testdata/picard/util/largeScattersNoRemainder/temp_0020_of_20/scattered.interval_list new file mode 100644 index 0000000000..e2306f582c --- /dev/null +++ b/testdata/picard/util/largeScattersNoRemainder/temp_0020_of_20/scattered.interval_list @@ -0,0 +1,13 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersNoRemainder --SCATTER_COUNT 20 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 24166721 24294271 + target_191 +chr1 24294272 24421820 + target_192 +chr1 24421821 24543637 + target_193 +chr1 24543638 24665452 + target_194 +chr1 24665453 24822768 + target_195 +chr1 24822769 24980083 + target_196 +chr1 24980084 25097392 + target_197 +chr1 25097393 25214699 + target_198 +chr1 25214700 25374885 + target_199 +chr1 25374886 25535069 + target_200 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0001_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0001_of_67/scattered.interval_list new file mode 100644 index 0000000000..1ccc0f5093 --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0001_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 1 195878 + target_1 +chr1 195879 391754 + target_2 +chr1 391755 606302 + target_3 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0002_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0002_of_67/scattered.interval_list new file mode 100644 index 0000000000..bc241235c5 --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0002_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 606303 820848 + target_4 +chr1 820849 910849 + target_5 +chr1 910850 1000848 + target_6 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0003_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0003_of_67/scattered.interval_list new file mode 100644 index 0000000000..209580106c --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0003_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 1000849 1112599 + target_7 +chr1 1112600 1224349 + target_8 +chr1 1224350 1348642 + target_9 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0004_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0004_of_67/scattered.interval_list new file mode 100644 index 0000000000..64b6584219 --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0004_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 1348643 1472934 + target_10 +chr1 1472935 1584197 + target_11 +chr1 1584198 1695459 + target_12 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0005_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0005_of_67/scattered.interval_list new file mode 100644 index 0000000000..2090c493c1 --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0005_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 1695460 1815724 + target_13 +chr1 1815725 1935987 + target_14 +chr1 1935988 2030188 + target_15 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0006_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0006_of_67/scattered.interval_list new file mode 100644 index 0000000000..70e1943991 --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0006_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 2030189 2124387 + target_16 +chr1 2124388 2261379 + target_17 +chr1 2261380 2398369 + target_18 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0007_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0007_of_67/scattered.interval_list new file mode 100644 index 0000000000..676af8bae5 --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0007_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 2398370 2662724 + target_19 +chr1 2662725 2927077 + target_20 +chr1 2927078 3044965 + target_21 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0008_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0008_of_67/scattered.interval_list new file mode 100644 index 0000000000..9803cb2fbf --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0008_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 3044966 3162852 + target_22 +chr1 3162853 3261512 + target_23 +chr1 3261513 3360170 + target_24 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0009_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0009_of_67/scattered.interval_list new file mode 100644 index 0000000000..cb2d9450d1 --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0009_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 3360171 3481821 + target_25 +chr1 3481822 3603470 + target_26 +chr1 3603471 3720976 + target_27 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0010_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0010_of_67/scattered.interval_list new file mode 100644 index 0000000000..df1bd3f9a4 --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0010_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 3720977 3838480 + target_28 +chr1 3838481 3931034 + target_29 +chr1 3931035 4023586 + target_30 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0011_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0011_of_67/scattered.interval_list new file mode 100644 index 0000000000..c9bfc9bd02 --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0011_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 4023587 4132844 + target_31 +chr1 4132845 4242101 + target_32 +chr1 4242102 4345574 + target_33 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0012_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0012_of_67/scattered.interval_list new file mode 100644 index 0000000000..9b9baa97f3 --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0012_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 4345575 4449046 + target_34 +chr1 4449047 4543247 + target_35 +chr1 4543248 4637446 + target_36 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0013_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0013_of_67/scattered.interval_list new file mode 100644 index 0000000000..19f6867974 --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0013_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 4637447 4761514 + target_37 +chr1 4761515 4885581 + target_38 +chr1 4885582 5011314 + target_39 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0014_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0014_of_67/scattered.interval_list new file mode 100644 index 0000000000..87471aa8dc --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0014_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 5011315 5137046 + target_40 +chr1 5137047 5243668 + target_41 +chr1 5243669 5350289 + target_42 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0015_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0015_of_67/scattered.interval_list new file mode 100644 index 0000000000..10128b89a5 --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0015_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 5350290 5485729 + target_43 +chr1 5485730 5621168 + target_44 +chr1 5621169 5745096 + target_45 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0016_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0016_of_67/scattered.interval_list new file mode 100644 index 0000000000..6c4ff761a1 --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0016_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 5745097 5869022 + target_46 +chr1 5869023 6009743 + target_47 +chr1 6009744 6150463 + target_48 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0017_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0017_of_67/scattered.interval_list new file mode 100644 index 0000000000..93a8e97e02 --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0017_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 6150464 6288718 + target_49 +chr1 6288719 6426971 + target_50 +chr1 6426972 6569464 + target_51 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0018_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0018_of_67/scattered.interval_list new file mode 100644 index 0000000000..cd0b262292 --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0018_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 6569465 6711955 + target_52 +chr1 6711956 6864915 + target_53 +chr1 6864916 7017874 + target_54 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0019_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0019_of_67/scattered.interval_list new file mode 100644 index 0000000000..c72dd38027 --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0019_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 7017875 7160373 + target_55 +chr1 7160374 7302870 + target_56 +chr1 7302871 7411540 + target_57 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0020_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0020_of_67/scattered.interval_list new file mode 100644 index 0000000000..0abb9a1258 --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0020_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 7411541 7520208 + target_58 +chr1 7520209 7670001 + target_59 +chr1 7670002 7819792 + target_60 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0021_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0021_of_67/scattered.interval_list new file mode 100644 index 0000000000..a61fdfc71f --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0021_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 7819793 7955554 + target_61 +chr1 7955555 8091315 + target_62 +chr1 8091316 8192379 + target_63 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0022_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0022_of_67/scattered.interval_list new file mode 100644 index 0000000000..9a02e214e3 --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0022_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 8192380 8293442 + target_64 +chr1 8293443 8451663 + target_65 +chr1 8451664 8609883 + target_66 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0023_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0023_of_67/scattered.interval_list new file mode 100644 index 0000000000..eb6db9f696 --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0023_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 8609884 8776005 + target_67 +chr1 8776006 8942125 + target_68 +chr1 8942126 9066968 + target_69 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0024_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0024_of_67/scattered.interval_list new file mode 100644 index 0000000000..2b25d14c90 --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0024_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 9066969 9191810 + target_70 +chr1 9191811 9290757 + target_71 +chr1 9290758 9389703 + target_72 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0025_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0025_of_67/scattered.interval_list new file mode 100644 index 0000000000..63d4a07e90 --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0025_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 9389704 9530072 + target_73 +chr1 9530073 9670439 + target_74 +chr1 9670440 9851576 + target_75 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0026_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0026_of_67/scattered.interval_list new file mode 100644 index 0000000000..237627ce3c --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0026_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 9851577 10032712 + target_76 +chr1 10032713 10183181 + target_77 +chr1 10183182 10333649 + target_78 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0027_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0027_of_67/scattered.interval_list new file mode 100644 index 0000000000..732d2e7c5e --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0027_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 10333650 10457488 + target_79 +chr1 10457489 10581325 + target_80 +chr1 10581326 10749793 + target_81 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0028_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0028_of_67/scattered.interval_list new file mode 100644 index 0000000000..366be0d7e0 --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0028_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 10749794 10918259 + target_82 +chr1 10918260 11027532 + target_83 +chr1 11027533 11136803 + target_84 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0029_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0029_of_67/scattered.interval_list new file mode 100644 index 0000000000..bc86dba62b --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0029_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 11136804 11280317 + target_85 +chr1 11280318 11423830 + target_86 +chr1 11423831 11549522 + target_87 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0030_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0030_of_67/scattered.interval_list new file mode 100644 index 0000000000..7ed85b3ccd --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0030_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 11549523 11675212 + target_88 +chr1 11675213 11776165 + target_89 +chr1 11776166 11877116 + target_90 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0031_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0031_of_67/scattered.interval_list new file mode 100644 index 0000000000..dca384f06a --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0031_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 11877117 12000862 + target_91 +chr1 12000863 12124606 + target_92 +chr1 12124607 12343496 + target_93 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0032_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0032_of_67/scattered.interval_list new file mode 100644 index 0000000000..9e18ccaa0d --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0032_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 12343497 12562384 + target_94 +chr1 12562385 12694554 + target_95 +chr1 12694555 12826723 + target_96 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0033_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0033_of_67/scattered.interval_list new file mode 100644 index 0000000000..3456645c7b --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0033_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 12826724 13005745 + target_97 +chr1 13005746 13184766 + target_98 +chr1 13184767 13327643 + target_99 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0034_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0034_of_67/scattered.interval_list new file mode 100644 index 0000000000..0de556b267 --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0034_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 13327644 13470518 + target_100 +chr1 13470519 13566626 + target_101 +chr1 13566627 13662732 + target_102 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0035_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0035_of_67/scattered.interval_list new file mode 100644 index 0000000000..b9cfe0fd90 --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0035_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 13662733 13806001 + target_103 +chr1 13806002 13949268 + target_104 +chr1 13949269 14043588 + target_105 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0036_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0036_of_67/scattered.interval_list new file mode 100644 index 0000000000..e3e0fa5a27 --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0036_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 14043589 14137907 + target_106 +chr1 14137908 14272203 + target_107 +chr1 14272204 14406498 + target_108 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0037_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0037_of_67/scattered.interval_list new file mode 100644 index 0000000000..94f4bcd9cf --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0037_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 14406499 14551515 + target_109 +chr1 14551516 14696530 + target_110 +chr1 14696531 14813755 + target_111 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0038_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0038_of_67/scattered.interval_list new file mode 100644 index 0000000000..3bcbc41d92 --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0038_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 14813756 14930979 + target_112 +chr1 14930980 15035314 + target_113 +chr1 15035315 15139648 + target_114 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0039_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0039_of_67/scattered.interval_list new file mode 100644 index 0000000000..1d7b2fc194 --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0039_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 15139649 15237194 + target_115 +chr1 15237195 15334738 + target_116 +chr1 15334739 15458284 + target_117 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0040_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0040_of_67/scattered.interval_list new file mode 100644 index 0000000000..3064887fd9 --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0040_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 15458285 15581828 + target_118 +chr1 15581829 15703637 + target_119 +chr1 15703638 15825445 + target_120 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0041_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0041_of_67/scattered.interval_list new file mode 100644 index 0000000000..51508f514e --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0041_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 15825446 15939965 + target_121 +chr1 15939966 16054483 + target_122 +chr1 16054484 16171468 + target_123 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0042_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0042_of_67/scattered.interval_list new file mode 100644 index 0000000000..34662883b0 --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0042_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 16171469 16288452 + target_124 +chr1 16288453 16398909 + target_125 +chr1 16398910 16509364 + target_126 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0043_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0043_of_67/scattered.interval_list new file mode 100644 index 0000000000..aa7e57aca0 --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0043_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 16509365 16549703 + target_127 +chr1 16549704 16590041 + target_128 +chr1 16590042 16638247 + target_129 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0044_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0044_of_67/scattered.interval_list new file mode 100644 index 0000000000..94ebfbc957 --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0044_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 16638248 16686451 + target_130 +chr1 16686452 16742020 + target_131 +chr1 16742021 16797588 + target_132 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0045_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0045_of_67/scattered.interval_list new file mode 100644 index 0000000000..727fd887f7 --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0045_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 16797589 16883908 + target_133 +chr1 16883909 16970227 + target_134 +chr1 16970228 17089415 + target_135 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0046_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0046_of_67/scattered.interval_list new file mode 100644 index 0000000000..dd2a58f8b8 --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0046_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 17089416 17208601 + target_136 +chr1 17208602 17303634 + target_137 +chr1 17303635 17398666 + target_138 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0047_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0047_of_67/scattered.interval_list new file mode 100644 index 0000000000..45b2ebe053 --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0047_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 17398667 17535915 + target_139 +chr1 17535916 17673163 + target_140 +chr1 17673164 17803647 + target_141 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0048_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0048_of_67/scattered.interval_list new file mode 100644 index 0000000000..f5f1b80b1d --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0048_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 17803648 17934130 + target_142 +chr1 17934131 18055738 + target_143 +chr1 18055739 18177344 + target_144 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0049_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0049_of_67/scattered.interval_list new file mode 100644 index 0000000000..c5c4f09a0e --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0049_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 18177345 18305108 + target_145 +chr1 18305109 18432871 + target_146 +chr1 18432872 18559883 + target_147 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0050_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0050_of_67/scattered.interval_list new file mode 100644 index 0000000000..ea64e5383e --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0050_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 18559884 18686893 + target_148 +chr1 18686894 18797287 + target_149 +chr1 18797288 18907680 + target_150 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0051_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0051_of_67/scattered.interval_list new file mode 100644 index 0000000000..83e24a8a03 --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0051_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 18907681 19040869 + target_151 +chr1 19040870 19174057 + target_152 +chr1 19174058 19300251 + target_153 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0052_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0052_of_67/scattered.interval_list new file mode 100644 index 0000000000..365db6e240 --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0052_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 19300252 19426443 + target_154 +chr1 19426444 19524828 + target_155 +chr1 19524829 19623211 + target_156 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0053_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0053_of_67/scattered.interval_list new file mode 100644 index 0000000000..cc64cd95ee --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0053_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 19623212 19743520 + target_157 +chr1 19743521 19863828 + target_158 +chr1 19863829 20021799 + target_159 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0054_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0054_of_67/scattered.interval_list new file mode 100644 index 0000000000..256ce34a40 --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0054_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 20021800 20179768 + target_160 +chr1 20179769 20319195 + target_161 +chr1 20319196 20458621 + target_162 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0055_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0055_of_67/scattered.interval_list new file mode 100644 index 0000000000..11a3ee2dd4 --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0055_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 20458622 20576129 + target_163 +chr1 20576130 20693635 + target_164 +chr1 20693636 20871153 + target_165 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0056_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0056_of_67/scattered.interval_list new file mode 100644 index 0000000000..3fb760517c --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0056_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 20871154 21048670 + target_166 +chr1 21048671 21206463 + target_167 +chr1 21206464 21364254 + target_168 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0057_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0057_of_67/scattered.interval_list new file mode 100644 index 0000000000..1298403f5b --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0057_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 21364255 21466916 + target_169 +chr1 21466917 21569576 + target_170 +chr1 21569577 21693920 + target_171 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0058_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0058_of_67/scattered.interval_list new file mode 100644 index 0000000000..5b9d4003e4 --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0058_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 21693921 21818263 + target_172 +chr1 21818264 21912191 + target_173 +chr1 21912192 22006117 + target_174 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0059_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0059_of_67/scattered.interval_list new file mode 100644 index 0000000000..0c29c776a0 --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0059_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 22006118 22110817 + target_175 +chr1 22110818 22215516 + target_176 +chr1 22215517 22340628 + target_177 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0060_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0060_of_67/scattered.interval_list new file mode 100644 index 0000000000..a6a7c55100 --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0060_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 22340629 22465738 + target_178 +chr1 22465739 22607396 + target_179 +chr1 22607397 22749052 + target_180 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0061_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0061_of_67/scattered.interval_list new file mode 100644 index 0000000000..9bf98ad52f --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0061_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 22749053 22906130 + target_181 +chr1 22906131 23063207 + target_182 +chr1 23063208 23237804 + target_183 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0062_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0062_of_67/scattered.interval_list new file mode 100644 index 0000000000..2473e00b4e --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0062_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 23237805 23412399 + target_184 +chr1 23412400 23568271 + target_185 +chr1 23568272 23724141 + target_186 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0063_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0063_of_67/scattered.interval_list new file mode 100644 index 0000000000..817a1855ea --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0063_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 23724142 23849296 + target_187 +chr1 23849297 23974450 + target_188 +chr1 23974451 24070586 + target_189 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0064_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0064_of_67/scattered.interval_list new file mode 100644 index 0000000000..9639c7f5de --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0064_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 24070587 24166720 + target_190 +chr1 24166721 24294271 + target_191 +chr1 24294272 24421820 + target_192 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0065_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0065_of_67/scattered.interval_list new file mode 100644 index 0000000000..7e48b79f30 --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0065_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 24421821 24543637 + target_193 +chr1 24543638 24665452 + target_194 +chr1 24665453 24822768 + target_195 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0066_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0066_of_67/scattered.interval_list new file mode 100644 index 0000000000..0abc06840e --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0066_of_67/scattered.interval_list @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 24822769 24980083 + target_196 +chr1 24980084 25097392 + target_197 +chr1 25097393 25214699 + target_198 diff --git a/testdata/picard/util/largeScattersWithRemainder/temp_0067_of_67/scattered.interval_list b/testdata/picard/util/largeScattersWithRemainder/temp_0067_of_67/scattered.interval_list new file mode 100644 index 0000000000..23ae01b3ba --- /dev/null +++ b/testdata/picard/util/largeScattersWithRemainder/temp_0067_of_67/scattered.interval_list @@ -0,0 +1,5 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +@PG ID:1 CL:IntervalListTools --INPUT testdata/picard/util/test.hg38.200.interval_list --OUTPUT testdata/picard/util/largeScattersWithRemainder --SCATTER_CONTENT 3 --SUBDIVISION_MODE INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER --PADDING 0 --UNIQUE false --DONT_MERGE_ABUTTING false --SORT true --ACTION CONCAT --SCATTER_COUNT 1 --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr1 25214700 25374885 + target_199 +chr1 25374886 25535069 + target_200 diff --git a/testdata/picard/util/test.hg38.200.interval_list b/testdata/picard/util/test.hg38.200.interval_list new file mode 100644 index 0000000000..04322fe62c --- /dev/null +++ b/testdata/picard/util/test.hg38.200.interval_list @@ -0,0 +1,202 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens +chr1 1 195878 + target_1 +chr1 195879 391754 + target_2 +chr1 391755 606302 + target_3 +chr1 606303 820848 + target_4 +chr1 820849 910849 + target_5 +chr1 910850 1000848 + target_6 +chr1 1000849 1112599 + target_7 +chr1 1112600 1224349 + target_8 +chr1 1224350 1348642 + target_9 +chr1 1348643 1472934 + target_10 +chr1 1472935 1584197 + target_11 +chr1 1584198 1695459 + target_12 +chr1 1695460 1815724 + target_13 +chr1 1815725 1935987 + target_14 +chr1 1935988 2030188 + target_15 +chr1 2030189 2124387 + target_16 +chr1 2124388 2261379 + target_17 +chr1 2261380 2398369 + target_18 +chr1 2398370 2662724 + target_19 +chr1 2662725 2927077 + target_20 +chr1 2927078 3044965 + target_21 +chr1 3044966 3162852 + target_22 +chr1 3162853 3261512 + target_23 +chr1 3261513 3360170 + target_24 +chr1 3360171 3481821 + target_25 +chr1 3481822 3603470 + target_26 +chr1 3603471 3720976 + target_27 +chr1 3720977 3838480 + target_28 +chr1 3838481 3931034 + target_29 +chr1 3931035 4023586 + target_30 +chr1 4023587 4132844 + target_31 +chr1 4132845 4242101 + target_32 +chr1 4242102 4345574 + target_33 +chr1 4345575 4449046 + target_34 +chr1 4449047 4543247 + target_35 +chr1 4543248 4637446 + target_36 +chr1 4637447 4761514 + target_37 +chr1 4761515 4885581 + target_38 +chr1 4885582 5011314 + target_39 +chr1 5011315 5137046 + target_40 +chr1 5137047 5243668 + target_41 +chr1 5243669 5350289 + target_42 +chr1 5350290 5485729 + target_43 +chr1 5485730 5621168 + target_44 +chr1 5621169 5745096 + target_45 +chr1 5745097 5869022 + target_46 +chr1 5869023 6009743 + target_47 +chr1 6009744 6150463 + target_48 +chr1 6150464 6288718 + target_49 +chr1 6288719 6426971 + target_50 +chr1 6426972 6569464 + target_51 +chr1 6569465 6711955 + target_52 +chr1 6711956 6864915 + target_53 +chr1 6864916 7017874 + target_54 +chr1 7017875 7160373 + target_55 +chr1 7160374 7302870 + target_56 +chr1 7302871 7411540 + target_57 +chr1 7411541 7520208 + target_58 +chr1 7520209 7670001 + target_59 +chr1 7670002 7819792 + target_60 +chr1 7819793 7955554 + target_61 +chr1 7955555 8091315 + target_62 +chr1 8091316 8192379 + target_63 +chr1 8192380 8293442 + target_64 +chr1 8293443 8451663 + target_65 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