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Don't crash if the tracker is null. Reset the alternate alleles based on the alts present in the subset of samples. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3009 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2010-03-16 04:00:04 +00:00
parent 10e76abbbc
commit f20f78d77f
1 changed files with 35 additions and 24 deletions
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59
java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VCFSubsetWalker.java
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@ -32,7 +32,6 @@ public class VCFSubsetWalker extends RodWalker<ArrayList<VCFRecord>, VCFWriter>
private VCFWriter vwriter = null; private VCFWriter vwriter = null;
public void initializeWriter() { public void initializeWriter() {
Set<VCFHeaderLine> metaData = new HashSet<VCFHeaderLine>(); Set<VCFHeaderLine> metaData = new HashSet<VCFHeaderLine>();
metaData.add(new VCFHeaderLine("source", "VariantsToVCF")); metaData.add(new VCFHeaderLine("source", "VariantsToVCF"));
metaData.add(new VCFHeaderLine("reference", this.getToolkit().getArguments().referenceFile.getAbsolutePath())); metaData.add(new VCFHeaderLine("reference", this.getToolkit().getArguments().referenceFile.getAbsolutePath()));
@ -51,23 +50,25 @@ public class VCFSubsetWalker extends RodWalker<ArrayList<VCFRecord>, VCFWriter>
public ArrayList<VCFRecord> map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { public ArrayList<VCFRecord> map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
ArrayList<VCFRecord> records = new ArrayList<VCFRecord>(); ArrayList<VCFRecord> records = new ArrayList<VCFRecord>();
for (ReferenceOrderedDatum rod : tracker.getAllRods()) { if (tracker != null) {
if (rod instanceof RodVCF) { for (ReferenceOrderedDatum rod : tracker.getAllRods()) {
RodVCF vcfrod = (RodVCF) rod; if (rod instanceof RodVCF) {
VCFRecord record = vcfrod.mCurrentRecord; RodVCF vcfrod = (RodVCF) rod;
VCFRecord record = vcfrod.mCurrentRecord;
if (SAMPLES == null) { if (SAMPLES == null) {
SAMPLES = new HashSet<String>(); SAMPLES = new HashSet<String>();
SAMPLES.addAll(vcfrod.getHeader().getGenotypeSamples()); SAMPLES.addAll(vcfrod.getHeader().getGenotypeSamples());
}
if (VPATH != null && vwriter == null) {
initializeWriter();
}
//out.println(record.toStringEncoding(vcfrod.getHeader()));
records.add(record);
} }
if (VPATH != null && vwriter == null) {
initializeWriter();
}
//out.println(record.toStringEncoding(vcfrod.getHeader()));
records.add(record);
} }
} }
@ -80,20 +81,30 @@ public class VCFSubsetWalker extends RodWalker<ArrayList<VCFRecord>, VCFWriter>
private VCFRecord subsetRecord(VCFRecord record) { private VCFRecord subsetRecord(VCFRecord record) {
ArrayList<VCFGenotypeRecord> genotypeRecords = new ArrayList<VCFGenotypeRecord>(); ArrayList<VCFGenotypeRecord> genotypeRecords = new ArrayList<VCFGenotypeRecord>();
for ( VCFGenotypeRecord gr : record.getVCFGenotypeRecords() ) { HashSet<VCFGenotypeEncoding> genotypeEncodingSet = new HashSet<VCFGenotypeEncoding>();
//if (gr.getSampleName().equalsIgnoreCase(SAMPLE)) { for ( VCFGenotypeRecord gr : record.getVCFGenotypeRecords() ) {
if (SAMPLES.contains(gr.getSampleName())) { if (SAMPLES.contains(gr.getSampleName())) {
//out.println(gr.getSampleName() + " " + gr.toGenotypeString(record.getAlternateAlleles()));
genotypeRecords.add(gr); genotypeRecords.add(gr);
for (VCFGenotypeEncoding allele : gr.getAlleles()) {
if (!allele.getBases().equalsIgnoreCase(record.getReference())) {
genotypeEncodingSet.add(allele);
}
}
} }
} }
ArrayList<VCFGenotypeEncoding> genotypeEncodings = new ArrayList<VCFGenotypeEncoding>();
for (VCFGenotypeEncoding allele : genotypeEncodingSet) {
genotypeEncodings.add(allele);
}
VCFRecord subset = new VCFRecord(record.getReference(), VCFRecord subset = new VCFRecord(record.getReference(),
record.getLocation().getContig(), record.getLocation().getContig(),
(int) record.getLocation().getStart(), (int) record.getLocation().getStart(),
record.getID(), record.getID(),
record.getAlternateAlleles(), genotypeEncodings,
record.getQual(), record.getQual(),
record.getFilterString(), record.getFilterString(),
record.getInfoValues(), record.getInfoValues(),
@ -116,8 +127,8 @@ public class VCFSubsetWalker extends RodWalker<ArrayList<VCFRecord>, VCFWriter>
//if (isVariant && !subset.isFiltered()) { //if (isVariant && !subset.isFiltered()) {
if ((isVariant || INCLUDE_NON_VARIANTS) && (!subset.isFiltered() || INCLUDE_FILTERED)) { if ((isVariant || INCLUDE_NON_VARIANTS) && (!subset.isFiltered() || INCLUDE_FILTERED)) {
if (writer != null) { if (vwriter != null) {
writer.addRecord(subset); vwriter.addRecord(subset);
} else { } else {
out.println(subset.toStringEncoding(vheader)); out.println(subset.toStringEncoding(vheader));
} }
@ -128,8 +139,8 @@ public class VCFSubsetWalker extends RodWalker<ArrayList<VCFRecord>, VCFWriter>
} }
public void onTraversalDone(VCFWriter writer) { public void onTraversalDone(VCFWriter writer) {
if (writer != null) { if (vwriter != null) {
writer.close(); vwriter.close();
} }
} }
} }