Make truncating the histogram optional in CollectInsertSizeMetrics

src/main/java/picard/analysis/CollectInsertSizeMetrics.java

@@ -105,6 +105,9 @@ public class CollectInsertSizeMetrics extends SinglePassSamProgram {
  "truncated to a shorter range of sizes, the MIN_HISTOGRAM_WIDTH will enforce a minimum range.", optional=true)
  public Integer MIN_HISTOGRAM_WIDTH = null;
 
+ @Argument(shortName = "TR", doc="Do not truncate the insert size histogram.", optional = true)
+ public boolean DO_NOT_TRUNCATE_HISTOGRAMS = false;
+
  @Argument(shortName="M", doc="When generating the Histogram, discard any data categories (out of FR, TANDEM, RF) that have fewer than this " +
  "percentage of overall reads. (Range: 0 to 1).")
  public float MINIMUM_PCT = 0.05f;
@@ -146,6 +149,10 @@ protected String[] customCommandLineValidation() {
  IOUtil.assertFileIsWritable(OUTPUT);
  IOUtil.assertFileIsWritable(Histogram_FILE);
 
+ if (DO_NOT_TRUNCATE_HISTOGRAMS){
+ HISTOGRAM_WIDTH = Integer.MAX_VALUE;
+ }
+
  //Delegate actual collection to InsertSizeMetricCollector
  multiCollector = new InsertSizeMetricsCollector(METRIC_ACCUMULATION_LEVEL, header.getReadGroups(), MINIMUM_PCT,
  HISTOGRAM_WIDTH, MIN_HISTOGRAM_WIDTH, DEVIATIONS, INCLUDE_DUPLICATES);

src/main/java/picard/analysis/directed/InsertSizeMetricsCollector.java

@@ -183,15 +183,15 @@ public void addMetricsToFile(final MetricsFile<InsertSizeMetrics,Integer> file)
  }
 
  // Trim the Histogram down to get rid of outliers that would make the chart useless.
- final Histogram<Integer> trimmedHistogram = histogram; // alias it
- trimmedHistogram.trimByWidth(getWidthToTrimTo(metrics));
+ histogram.trimByWidth(getWidthToTrimTo(metrics));
 
- if (!trimmedHistogram.isEmpty()) {
- metrics.MEAN_INSERT_SIZE = trimmedHistogram.getMean();
- metrics.STANDARD_DEVIATION = trimmedHistogram.getStandardDeviation();
+ // Compute metrics that are sensitive to outliers after trimming.
+ if (!histogram.isEmpty()) {
+ metrics.MEAN_INSERT_SIZE = histogram.getMean();
+ metrics.STANDARD_DEVIATION = histogram.getStandardDeviation();
  }
 
- file.addHistogram(trimmedHistogram);
+ file.addHistogram(histogram);
  file.addMetric(metrics);
  }
  }

src/test/java/picard/analysis/CollectInsertSizeMetricsTest.java

@@ -30,6 +30,7 @@
 import htsjdk.samtools.metrics.MetricsFile;
 import org.testng.Assert;
 import org.testng.annotations.Test;
+import picard.PicardException;
 import picard.cmdline.CommandLineProgramTest;
 import picard.util.RExecutor;
 
@@ -248,6 +249,70 @@ public void testHistogramWidthIsSetProperly() throws IOException {
  Assert.assertEquals(output.getAllHistograms().size(), 5);
  }
 
+ @Test
+ public void testSkipTruncatingHistogram() throws IOException {
+ final SAMRecordSetBuilder setBuilder = new SAMRecordSetBuilder(true, SAMFileHeader.SortOrder.coordinate, true);
+ final int readLength = 10;
+ setBuilder.setReadLength(readLength);
+ final int minInsertSize = 100;
+ final int maxInsertSize = 400;
+ int readCount = 0;
+ final int start = 1000;
+ final String cigar = readLength + "M";
+ for (int j = minInsertSize; j < maxInsertSize; j++) {
+ setBuilder.addPair("read:" + readCount++, 0, start, start + j - readLength, false, false,
+ cigar, cigar, false, true, 60);
+ }
+
+ // Add an outlier
+ int outlierInsertSize = 2000;
+ setBuilder.addPair("outlierRead", 0, start, start + outlierInsertSize - readLength,
+ false, false, cigar, cigar, false, true, 60);
+
+ final File testSamFile = File.createTempFile("CollectInsertSizeMetrics", ".bam");
+ testSamFile.deleteOnExit();
+ final File testSamFileIndex = new File(testSamFile.getParentFile(),testSamFile.getName().replace("bam$","bai"));
+ testSamFileIndex.deleteOnExit();
+ try ( final SAMFileWriter writer = new SAMFileWriterFactory().setCreateIndex(true)
+ .makeBAMWriter(setBuilder.getHeader(), false, testSamFile)) {
+ setBuilder.forEach(writer::addAlignment);
+ }
+
+ final File outfile = File.createTempFile("test", ".insert_size_metrics");
+ final File pdf = File.createTempFile("test", ".pdf");
+ outfile.deleteOnExit();
+ pdf.deleteOnExit();
+ final String[] args = new String[]{
+ "INPUT=" + testSamFile.getAbsolutePath(),
+ "OUTPUT=" + outfile.getAbsolutePath(),
+ "Histogram_FILE=" + pdf.getAbsolutePath(),
+ "TR=" + true
+ };
+
+ Assert.assertEquals(runPicardCommandLine(args), 0);
+ final MetricsFile<InsertSizeMetrics, Comparable<?>> output = new MetricsFile<>();
+ output.read(new FileReader(outfile));
+
+ Assert.assertEquals(output.getAllHistograms().get(0).get(outlierInsertSize).getValue(), 1.0);
+
+ // Run again with truncation enabled
+ final File outfileWithTruncation = File.createTempFile("test", ".insert_size_metrics");
+ outfileWithTruncation.deleteOnExit();
+ final String[] argsWithTruncation = new String[]{
+ "INPUT=" + testSamFile.getAbsolutePath(),
+ "OUTPUT=" + outfileWithTruncation.getAbsolutePath(),
+ "Histogram_FILE=" + pdf.getAbsolutePath()
+ };
+
+ Assert.assertEquals(runPicardCommandLine(argsWithTruncation), 0);
+ final MetricsFile<InsertSizeMetrics, Comparable<?>> outputWithTruncation = new MetricsFile<>();
+ outputWithTruncation.read(new FileReader(outfileWithTruncation));
+
+ // Check that the outlier has been removed when truncation is enabled
+ Assert.assertFalse(outputWithTruncation.getAllHistograms().get(0).containsKey(outlierInsertSize));
+
+ }
+
  @Test
  public void testMultipleOrientationsForHistogram() throws IOException {
  final File output = new File("testdata/picard/analysis/directed/CollectInsertSizeMetrics", "multiple_orientation.sam.insert_size_metrics");
@@ -291,8 +356,6 @@ public void testWidthOfMetrics() throws IOException {
  testSamFileIndex.deleteOnExit();
 
 
- new File(testSamFile.getAbsolutePath().replace(".bam$",".bai")).deleteOnExit();
-
  final SAMRecordSetBuilder setBuilder = new SAMRecordSetBuilder(true, SAMFileHeader.SortOrder.coordinate, true);
  setBuilder.setReadLength(10);
 
@@ -326,7 +389,6 @@ public void testWidthOfMetrics() throws IOException {
  setBuilder.forEach(writer::addAlignment);
  writer.close();
 
-
  final File outfile = File.createTempFile("test", ".insert_size_metrics");
  final File pdf = File.createTempFile("test", ".pdf");
  outfile.deleteOnExit();