zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

59
java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VCFSubsetWalker.java
View File

@ -32,7 +32,6 @@ public class VCFSubsetWalker extends RodWalker<ArrayList<VCFRecord>, VCFWriter>
private VCFWriter vwriter = null;
public void initializeWriter() {
Set<VCFHeaderLine> metaData = new HashSet<VCFHeaderLine>();
metaData.add(new VCFHeaderLine("source", "VariantsToVCF"));
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) {
ArrayList<VCFRecord> records = new ArrayList<VCFRecord>();
for (ReferenceOrderedDatum rod : tracker.getAllRods()) {
if (rod instanceof RodVCF) {
RodVCF vcfrod = (RodVCF) rod;
VCFRecord record = vcfrod.mCurrentRecord;
if (tracker != null) {
for (ReferenceOrderedDatum rod : tracker.getAllRods()) {
if (rod instanceof RodVCF) {
RodVCF vcfrod = (RodVCF) rod;
VCFRecord record = vcfrod.mCurrentRecord;
if (SAMPLES == null) {
SAMPLES = new HashSet<String>();
SAMPLES.addAll(vcfrod.getHeader().getGenotypeSamples());
if (SAMPLES == null) {
SAMPLES = new HashSet<String>();
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) {
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())) {
//out.println(gr.getSampleName() + " " + gr.toGenotypeString(record.getAlternateAlleles()));
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(),
record.getLocation().getContig(),
(int) record.getLocation().getStart(),
record.getID(),
record.getAlternateAlleles(),
genotypeEncodings,
record.getQual(),
record.getFilterString(),
record.getInfoValues(),
@ -116,8 +127,8 @@ public class VCFSubsetWalker extends RodWalker<ArrayList<VCFRecord>, VCFWriter>
//if (isVariant && !subset.isFiltered()) {
if ((isVariant || INCLUDE_NON_VARIANTS) && (!subset.isFiltered() || INCLUDE_FILTERED)) {
if (writer != null) {
writer.addRecord(subset);
if (vwriter != null) {
vwriter.addRecord(subset);
} else {
out.println(subset.toStringEncoding(vheader));
}
@ -128,8 +139,8 @@ public class VCFSubsetWalker extends RodWalker<ArrayList<VCFRecord>, VCFWriter>
}
public void onTraversalDone(VCFWriter writer) {
if (writer != null) {
writer.close();
if (vwriter != null) {
vwriter.close();
}
}
}