despite efforts to the contrary, FingerprintChecker cannot fingerprin…

…ting sam files that have a mismatching dictionary from the one stated in the haplotype map (it works for vcfs). This is because when fingerprinting sam files, the SamLocusIterator is given an IntervalList to query, and this IL has a mismatching dictionary which isn't supported.

This PR resolves this by creating a new IL just before querying the Iterator using the proper dictionary.

src/main/java/picard/fingerprint/FingerprintChecker.java

@@ -535,7 +535,15 @@ public Map<FingerprintIdDetails, Fingerprint> fingerprintSamFile(final Path samF
             log.info(String.format("Reading an indexed file (%s)", samFile.toUri().toString()));
         }
 
-        final SamLocusIterator iterator = new SamLocusIterator(in, this.haplotypes.getIntervalList(), in.hasIndex());
+        // fingerprinting allows that headers differ, but SamLocusIterator doesn't allow the dictionary of the query
+        // interval list to differ from that of the samfile, leading to an exception thrown.
+        // At this point we already know that the dictionary of the haplotypes is a proper prefix of that of the sam file
+        // So we just swap out the header in the interval list.
+        final IntervalList il = this.haplotypes.getIntervalList();
+        final IntervalList newIl = new IntervalList(in.getFileHeader());
+        newIl.addall(il.getIntervals());
+
+        final SamLocusIterator iterator = new SamLocusIterator(in, newIl, in.hasIndex());
         iterator.setEmitUncoveredLoci(true);
         iterator.setMappingQualityScoreCutoff(this.minimumMappingQuality);
         iterator.setQualityScoreCutoff(this.minimumBaseQuality);

src/test/java/picard/fingerprint/CrosscheckFingerprintsTest.java

@@ -40,6 +40,7 @@ public class CrosscheckFingerprintsTest extends CommandLineProgramTest {
 
     private final File TEST_DATA_DIR = new File("testdata/picard/fingerprint/");
     private final File HAPLOTYPE_MAP = new File(TEST_DATA_DIR, "Homo_sapiens_assembly19.haplotype_database.subset.txt");
+    private final File HAPLOTYPE_MAP_SHORT = new File(TEST_DATA_DIR, "Homo_sapiens_assembly19.haplotype_database.subset.short_dictionary.txt");
     private final File HAPLOTYPE_MAP_FOR_CRAMS = new File(TEST_DATA_DIR, "Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt");
 
     private final File NA12891_r1_sam = new File(TEST_DATA_DIR, "NA12891.over.fingerprints.r1.sam");
@@ -201,6 +202,31 @@ public void testCrossCheckRGs(final File file1, final File file2, final boolean
         doTest(args.toArray(new String[0]), metrics, expectedRetVal, expectedNMetrics, CrosscheckMetric.DataType.READGROUP, expectAllMatch);
     }
 
+    @Test(dataProvider = "bamFilesRGs")
+    public void testCrossCheckRGs_with_short_dictionary(final File file1, final File file2, final boolean expectAllMatch, final int expectedRetVal, final int expectedNMetrics) throws IOException {
+
+        File metrics = File.createTempFile("Fingerprinting", "NA1291.RG.crosscheck_metrics");
+        metrics.deleteOnExit();
+
+        final List<String> args = new ArrayList<>(Arrays.asList("INPUT=" + file1.getAbsolutePath(),
+                "INPUT=" + file2.getAbsolutePath(),
+                "OUTPUT=" + metrics.getAbsolutePath(),
+                "LOD_THRESHOLD=" + -2.0,
+                "EXPECT_ALL_GROUPS_TO_MATCH=" + expectAllMatch)
+        );
+
+        if (file1.getName().endsWith(SamReader.Type.CRAM_TYPE.fileExtension())) {
+            args.add("R=" + referenceForCrams);
+            args.add("HAPLOTYPE_MAP=" + HAPLOTYPE_MAP_FOR_CRAMS);
+        } else {
+            args.add("HAPLOTYPE_MAP=" + HAPLOTYPE_MAP_SHORT);
+        }
+
+        doTest(args.toArray(new String[0]), metrics, expectedRetVal, expectedNMetrics, CrosscheckMetric.DataType.READGROUP, expectAllMatch);
+    }
+
+
+
     @DataProvider(name = "cramsWithNoReference")
     public Object[][] cramsWithNoReference() {
         return new Object[][]{

testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.short_dictionary.txt

@@ -0,0 +1,16 @@
+@HD	VN:1.4	GO:none	SO:coordinate
+@SQ	SN:1	LN:249250621	AS:GRCh37	UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta	M5:1b22b98cdeb4a9304cb5d48026a85128	SP:Homo Sapiens
+@SQ	SN:2	LN:243199373	AS:GRCh37	UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta	M5:a0d9851da00400dec1098a9255ac712e	SP:Homo Sapiens
+@SQ	SN:3	LN:198022430	AS:GRCh37	UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta	M5:fdfd811849cc2fadebc929bb925902e5	SP:Homo Sapiens
+@SQ	SN:4	LN:191154276	AS:GRCh37	UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta	M5:23dccd106897542ad87d2765d28a19a1	SP:Homo Sapiens
+@SQ	SN:5	LN:180915260	AS:GRCh37	UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta	M5:0740173db9ffd264d728f32784845cd7	SP:Homo Sapiens
+@SQ	SN:6	LN:171115067	AS:GRCh37	UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta	M5:1d3a93a248d92a729ee764823acbbc6b	SP:Homo Sapiens
+@SQ	SN:7	LN:159138663	AS:GRCh37	UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta	M5:618366e953d6aaad97dbe4777c29375e	SP:Homo Sapiens
+@SQ	SN:8	LN:146364022	AS:GRCh37	UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta	M5:96f514a9929e410c6651697bded59aec	SP:Homo Sapiens
+@SQ	SN:9	LN:141213431	AS:GRCh37	UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta	M5:3e273117f15e0a400f01055d9f393768	SP:Homo Sapiens
+#CHROMOSOME	POSITION	NAME	MAJOR_ALLELE	MINOR_ALLELE	MAF	ANCHOR_SNP	PANELS
+1	14804874	rs7555566	A	G	0.223794		
+3	17077268	rs17272796	C	T	0.623026		
+4	57194525	rs6834736	C	G	0.512884		
+5	156355375	rs2862058	A	G	0.349127		
+7	4490854	rs314605	C	T	0.786367