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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Guillermo del Angel 2012-02-25 13:57:54 -05:00
parent dea35943d1 c8a06e53c1
commit 16122bea8d
8 changed files with 118 additions and 46 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;
}

4
public/java/src/org/broadinstitute/sting/utils/Haplotype.java
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@ -28,9 +28,7 @@ import net.sf.samtools.Cigar;
import net.sf.samtools.CigarElement;
import net.sf.samtools.CigarOperator;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import java.util.Arrays;
@ -133,7 +131,7 @@ public class Haplotype {
}
} else if( refAllele.length() < altAllele.length() ) { // insertion
final int altAlleleLength = altAllele.length();
for( int iii = newHaplotype.length -1; iii > haplotypeInsertLocation + altAlleleLength; iii-- ) {
for( int iii = newHaplotype.length - 1; iii > haplotypeInsertLocation + altAlleleLength - 1; iii-- ) {
newHaplotype[iii] = newHaplotype[iii-altAlleleLength];
}
for( int iii = 0; iii < altAlleleLength; iii++ ) {

7
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
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@ -544,12 +544,15 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
}
/**
* return true if this is a symbolic allele (e.g. <SOMETAG>) otherwise false
* return true if this is a symbolic allele (e.g. <SOMETAG>) or
* structural variation breakend (with [ or ]), otherwise false
* @param allele the allele to check
* @return true if the allele is a symbolic allele, otherwise false
*/
private static boolean isSymbolicAllele(String allele) {
return (allele != null && allele.startsWith("<") && allele.endsWith(">") && allele.length() > 2);
return (allele != null && allele.length() > 2 &&
((allele.startsWith("<") && allele.endsWith(">")) ||
(allele.contains("[") || allele.contains("]"))));
}
/**

6
public/java/src/org/broadinstitute/sting/utils/sam/AlignmentStartWithNoTiesComparator.java
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@ -36,8 +36,10 @@ public class AlignmentStartWithNoTiesComparator implements Comparator<SAMRecord>
result = cmpContig;
else {
if (r1.getAlignmentStart() < r2.getAlignmentStart()) result = -1;
else result = 1;
if (r1.getAlignmentStart() < r2.getAlignmentStart())
result = -1;
else
result = 1;
}
}

8
public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java
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@ -212,7 +212,13 @@ public class Allele implements Comparable<Allele> {
* @return true if the bases represent a symbolic allele
*/
public static boolean wouldBeSymbolicAllele(byte[] bases) {
return bases.length > 2 && bases[0] == '<' && bases[bases.length-1] == '>';
if ( bases.length <= 2 )
return false;
else {
final String strBases = new String(bases);
return (bases[0] == '<' && bases[bases.length-1] == '>') ||
(strBases.contains("[") || strBases.contains("]"));
}
}
/**

10
public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java
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@ -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"); }
}

16
public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java
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@ -9,7 +9,7 @@ import java.util.List;
public class VCFIntegrationTest extends WalkerTest {
@Test
@Test(enabled = true)
public void testReadingAndWritingWitHNoChanges() {
String md5ofInputVCF = "a990ba187a69ca44cb9bc2bb44d00447";
@ -25,4 +25,18 @@ public class VCFIntegrationTest extends WalkerTest {
WalkerTestSpec spec2 = new WalkerTestSpec(test2, 1, Arrays.asList(md5ofInputVCF));
executeTest("Test Variants To VCF from new output", spec2);
}
@Test
// See https://getsatisfaction.com/gsa/topics/support_vcf_4_1_structural_variation_breakend_alleles?utm_content=topic_link&utm_medium=email&utm_source=new_topic
public void testReadingAndWritingBreakpointAlleles() {
String testVCF = testDir + "breakpoint-example.vcf";
//String testVCF = validationDataLocation + "multiallelic.vcf";
String baseCommand = "-R " + b37KGReference + " -NO_HEADER -o %s ";
String test1 = baseCommand + "-T SelectVariants -V " + testVCF;
WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("76075307afd26b4db6234795d9fb3c2f"));
executeTest("Test reading and writing breakpoint VCF", spec1);
}
}

6
public/testdata/breakpoint-example.vcf vendored 100644
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@ -0,0 +1,6 @@
##fileformat=VCFv4.1
#CHROM POS ID REF ALT QUAL FILTER INFO
22 50 bnd_W G G]22:6000] 6 PASS SVTYPE=BND;MATEID=bnd_Y
22 51 bnd_V T ]22:55]T 6 PASS SVTYPE=BND;MATEID=bnd_U
22 55 bnd_U C C[22:51[ 6 PASS SVTYPE=BND;MATEID=bnd_V
22 6000 bnd_Y A A]22:50] 6 PASS SVTYPE=BND;MATEID=bnd_W