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Replaced SSG with UG in packaging utils. Minor performance and formatting improvements for ClipReads 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1882 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-10-20 01:19:58 +00:00
parent c29924e7cf
commit a8a2c1a2a1
2 changed files with 5 additions and 7 deletions
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10
java/src/org/broadinstitute/sting/playground/gatk/walkers/ClipReadsWalker.java
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@ -59,9 +59,6 @@ public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipper, Cli
@Argument(fullName = "outputBam", shortName = "ob", doc = "Write output to this BAM filename instead of STDOUT", required = false) @Argument(fullName = "outputBam", shortName = "ob", doc = "Write output to this BAM filename instead of STDOUT", required = false)
String outputBamFile = null; String outputBamFile = null;
@Argument(fullName = "", shortName = "STD", doc = "FOR DEBUGGING ONLY", required = false)
boolean toStandardOut = false;
@Argument(fullName = "qTrimmingThreshold", shortName = "QT", doc = "", required = false) @Argument(fullName = "qTrimmingThreshold", shortName = "QT", doc = "", required = false)
int qTrimmingThreshold = -1; int qTrimmingThreshold = -1;
@ -304,9 +301,10 @@ public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipper, Cli
public ClippingData reduceInit() { public ClippingData reduceInit() {
SAMFileWriter outputBam = null; SAMFileWriter outputBam = null;
if ( outputBamFile != null && ! toStandardOut ) { if ( outputBamFile != null ) {
SAMFileHeader header = this.getToolkit().getSAMFileHeader(); SAMFileHeader header = this.getToolkit().getSAMFileHeader();
outputBam = Utils.createSAMFileWriterWithCompression(header, false, outputBamFile, 5); boolean maintainsSort = clippingRepresentation != ClippingRepresentation.SOFTCLIP_BASES;
outputBam = Utils.createSAMFileWriterWithCompression(header, maintainsSort, outputBamFile, 5);
} }
return new ClippingData(outputBam, sequencesToClip); return new ClippingData(outputBam, sequencesToClip);
@ -315,7 +313,7 @@ public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipper, Cli
public ClippingData reduce(ReadClipper clipper, ClippingData data) { public ClippingData reduce(ReadClipper clipper, ClippingData data) {
if (data.output != null) { if (data.output != null) {
data.output.addAlignment(clipper.clipRead(clippingRepresentation)); data.output.addAlignment(clipper.clipRead(clippingRepresentation));
} else if (toStandardOut) { } else {
out.println(clipper.clipRead(clippingRepresentation).format()); out.println(clipper.clipRead(clippingRepresentation).format());
} }

2
packages/GenomeAnalysisTK.xml
View File

@ -24,7 +24,7 @@
<!-- Variant filtration --> <!-- Variant filtration -->
<class>org.broadinstitute.sting.gatk.walkers.filters.VariantFiltrationWalker</class> <class>org.broadinstitute.sting.gatk.walkers.filters.VariantFiltrationWalker</class>
<!-- Single sample genotyper --> <!-- Single sample genotyper -->
<class>org.broadinstitute.sting.gatk.walkers.genotyper.SingleSampleGenotyper</class> <class>org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper</class>
<!-- And the filters --> <!-- And the filters -->
<class>org.broadinstitute.sting.gatk.walkers.filters.IVFSecondaryBases</class> <class>org.broadinstitute.sting.gatk.walkers.filters.IVFSecondaryBases</class>
<class>org.broadinstitute.sting.gatk.walkers.filters.VECFisherStrand</class> <class>org.broadinstitute.sting.gatk.walkers.filters.VECFisherStrand</class>