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DoC now properly handles reference N bases + misc. additional cleanups 

-- DoC now by default ignores bases with reference Ns, so these are not included in the coverage calculations at any stage.
-- Added option --includeRefNSites that will include them in the calculation
-- Added integration tests that ensures the per base tables (and so all subsequent calculations) work with and without reference N bases included
-- Reorganized command line options, tagging advanced options with @Advanced
This commit is contained in:
Mark DePristo 2012-02-25 11:32:50 -05:00
parent 50de1a3eab
commit c8a06e53c1
2 changed files with 80 additions and 37 deletions
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107
public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
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@ -26,6 +26,7 @@
package org.broadinstitute.sting.gatk.walkers.coverage;
import net.sf.samtools.SAMReadGroupRecord;
import org.broadinstitute.sting.commandline.Advanced;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@ -119,21 +120,6 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<DoCOutputType.Partiti
@Multiplex(value=DoCOutputMultiplexer.class,arguments={"partitionTypes","refSeqGeneList","omitDepthOutput","omitIntervals","omitSampleSummary","omitLocusTable"})
Map<DoCOutputType,PrintStream> out;
/**
* Sets the low-coverage cutoff for granular binning. All loci with depth < START are counted in the first bin.
*/
@Argument(fullName = "start", doc = "Starting (left endpoint) for granular binning", required = false)
int start = 1;
/**
* Sets the high-coverage cutoff for granular binning. All loci with depth > END are counted in the last bin.
*/
@Argument(fullName = "stop", doc = "Ending (right endpoint) for granular binning", required = false)
int stop = 500;
/**
* Sets the number of bins for granular binning
*/
@Argument(fullName = "nBins", doc = "Number of bins to use for granular binning", required = false)
int nBins = 499;
@Argument(fullName = "minMappingQuality", shortName = "mmq", doc = "Minimum mapping quality of reads to count towards depth. Defaults to -1.", required = false)
int minMappingQuality = -1;
@Argument(fullName = "maxMappingQuality", doc = "Maximum mapping quality of reads to count towards depth. Defaults to 2^31-1 (Integer.MAX_VALUE).", required = false)
@ -142,16 +128,19 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<DoCOutputType.Partiti
byte minBaseQuality = -1;
@Argument(fullName = "maxBaseQuality", doc = "Maximum quality of bases to count towards depth. Defaults to 127 (Byte.MAX_VALUE).", required = false)
byte maxBaseQuality = Byte.MAX_VALUE;
/**
* Instead of reporting depth, report the base pileup at each locus
*/
@Argument(fullName = "printBaseCounts", shortName = "baseCounts", doc = "Will add base counts to per-locus output.", required = false)
boolean printBaseCounts = false;
/**
* Do not tabulate locus statistics (# loci covered by sample by coverage)
*/
@Argument(fullName = "omitLocusTable", shortName = "omitLocusTable", doc = "Will not calculate the per-sample per-depth counts of loci, which should result in speedup", required = false)
boolean omitLocusTable = false;
/**
* Do not tabulate interval statistics (mean, median, quartiles AND # intervals by sample by coverage)
*/
@ -162,8 +151,52 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<DoCOutputType.Partiti
*/
@Argument(fullName = "omitDepthOutputAtEachBase", shortName = "omitBaseOutput", doc = "Will omit the output of the depth of coverage at each base, which should result in speedup", required = false)
boolean omitDepthOutput = false;
/**
* Path to the RefSeq file for use in aggregating coverage statistics over genes
*/
@Argument(fullName = "calculateCoverageOverGenes", shortName = "geneList", doc = "Calculate the coverage statistics over this list of genes. Currently accepts RefSeq.", required = false)
File refSeqGeneList = null;
/**
* The format of the output file
*/
@Argument(fullName = "outputFormat", doc = "the format of the output file (e.g. csv, table, rtable); defaults to r-readable table", required = false)
String outputFormat = "rtable";
// ---------------------------------------------------------------------------
//
// Advanced arguments
//
// ---------------------------------------------------------------------------
@Advanced
@Argument(fullName = "includeRefNSites", doc = "If provided, sites with reference N bases but with coverage from neighboring reads will be included in DoC calculations.", required = false)
boolean includeRefNBases = false;
@Advanced
@Argument(fullName = "printBinEndpointsAndExit", doc = "Prints the bin values and exits immediately. Use to calibrate what bins you want before running on data.", required = false)
boolean printBinEndpointsAndExit = false;
/**
* Sets the low-coverage cutoff for granular binning. All loci with depth < START are counted in the first bin.
*/
@Advanced
@Argument(fullName = "start", doc = "Starting (left endpoint) for granular binning", required = false)
int start = 1;
/**
* Sets the high-coverage cutoff for granular binning. All loci with depth > END are counted in the last bin.
*/
@Advanced
@Argument(fullName = "stop", doc = "Ending (right endpoint) for granular binning", required = false)
int stop = 500;
/**
* Sets the number of bins for granular binning
*/
@Advanced
@Argument(fullName = "nBins", doc = "Number of bins to use for granular binning", required = false)
int nBins = 499;
/**
* Do not tabulate the sample summary statistics (total, mean, median, quartile coverage per sample)
*/
@ -174,27 +207,22 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<DoCOutputType.Partiti
*/
@Argument(fullName = "partitionType", shortName = "pt", doc = "Partition type for depth of coverage. Defaults to sample. Can be any combination of sample, readgroup, library.", required = false)
Set<DoCOutputType.Partition> partitionTypes = EnumSet.of(DoCOutputType.Partition.sample);
/**
* Consider a spanning deletion as contributing to coverage. Also enables deletion counts in per-base output.
*/
@Advanced
@Argument(fullName = "includeDeletions", shortName = "dels", doc = "Include information on deletions", required = false)
boolean includeDeletions = false;
@Advanced
@Argument(fullName = "ignoreDeletionSites", doc = "Ignore sites consisting only of deletions", required = false)
boolean ignoreDeletionSites = false;
/**
* Path to the RefSeq file for use in aggregating coverage statistics over genes
*/
@Argument(fullName = "calculateCoverageOverGenes", shortName = "geneList", doc = "Calculate the coverage statistics over this list of genes. Currently accepts RefSeq.", required = false)
File refSeqGeneList = null;
/**
* The format of the output file
*/
@Argument(fullName = "outputFormat", doc = "the format of the output file (e.g. csv, table, rtable); defaults to r-readable table", required = false)
String outputFormat = "rtable";
/**
* A coverage threshold for summarizing (e.g. % bases >= CT for each sample)
*/
@Advanced
@Argument(fullName = "summaryCoverageThreshold", shortName = "ct", doc = "for summary file outputs, report the % of bases coverd to >= this number. Defaults to 15; can take multiple arguments.", required = false)
int[] coverageThresholds = {15};
@ -334,24 +362,29 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<DoCOutputType.Partiti
}
public Map<DoCOutputType.Partition,Map<String,int[]>> map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if (includeRefNBases || BaseUtils.isRegularBase(ref.getBase())) {
if ( ! omitDepthOutput ) {
getCorrectStream(null, DoCOutputType.Aggregation.locus, DoCOutputType.FileType.summary).printf("%s",ref.getLocus()); // yes: print locus in map, and the rest of the info in reduce (for eventual cumulatives)
//System.out.printf("\t[log]\t%s",ref.getLocus());
}
if ( ! omitDepthOutput ) {
getCorrectStream(null, DoCOutputType.Aggregation.locus, DoCOutputType.FileType.summary).printf("%s",ref.getLocus()); // yes: print locus in map, and the rest of the info in reduce (for eventual cumulatives)
//System.out.printf("\t[log]\t%s",ref.getLocus());
return CoverageUtils.getBaseCountsByPartition(context,minMappingQuality,maxMappingQuality,minBaseQuality,maxBaseQuality,partitionTypes);
} else {
return null;
}
return CoverageUtils.getBaseCountsByPartition(context,minMappingQuality,maxMappingQuality,minBaseQuality,maxBaseQuality,partitionTypes);
}
public CoveragePartitioner reduce(Map<DoCOutputType.Partition,Map<String,int[]>> thisMap, CoveragePartitioner prevReduce) {
if ( ! omitDepthOutput ) {
//checkOrder(prevReduce); // tests prevReduce.getIdentifiersByType().get(t) against the initialized header order
printDepths(getCorrectStream(null, DoCOutputType.Aggregation.locus, DoCOutputType.FileType.summary),thisMap,prevReduce.getIdentifiersByType());
// this is an additional iteration through thisMap, plus dealing with IO, so should be much slower without
// turning on omit
}
if ( thisMap != null ) { // skip sites we didn't want to include in the calculation (ref Ns)
if ( ! omitDepthOutput ) {
//checkOrder(prevReduce); // tests prevReduce.getIdentifiersByType().get(t) against the initialized header order
printDepths(getCorrectStream(null, DoCOutputType.Aggregation.locus, DoCOutputType.FileType.summary),thisMap,prevReduce.getIdentifiersByType());
// this is an additional iteration through thisMap, plus dealing with IO, so should be much slower without
// turning on omit
}
prevReduce.update(thisMap); // note that in "useBoth" cases, this method alters the thisMap object
prevReduce.update(thisMap); // note that in "useBoth" cases, this method alters the thisMap object
}
return prevReduce;
}

10
public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java
View File

@ -94,4 +94,14 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest {
execute("testNoCoverageDueToFiltering",spec);
}
public void testRefNHandling(boolean includeNs, final String md5) {
String command = "-R " + b37KGReference + " -L 20:26,319,565-26,319,575 -I " + validationDataLocation + "NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.20.bam -T DepthOfCoverage -baseCounts --omitIntervalStatistics --omitLocusTable --omitPerSampleStats -o %s";
if ( includeNs ) command += " --includeRefNSites";
WalkerTestSpec spec = new WalkerTestSpec(command, 1, Arrays.asList(md5));
executeTest("Testing DoC " + (includeNs ? "with" : "without") + " reference Ns", spec);
}
@Test public void testRefNWithNs() { testRefNHandling(true, "24cd2da2e4323ce6fd76217ba6dc2834"); }
@Test public void testRefNWithoutNs() { testRefNHandling(false, "4fc0f1a2e968f777d693abcefd4fb7af"); }
}