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Useful utility function to print out the Allele as a String since toString prints out * for refs. It was annoying to keep seeing new String(Allele.getBases()). 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3989 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-08-09 20:35:56 +00:00
parent d0ecb8875a
commit 0eeb659aa3
3 changed files with 6 additions and 7 deletions
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4
java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
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@ -598,7 +598,7 @@ public class VariantContextUtils {
for (Allele a : inputVC.getAlleles()) { for (Allele a : inputVC.getAlleles()) {
// get bases for current allele and create a new one with trimmed bases // get bases for current allele and create a new one with trimmed bases
String newBases = new String(new byte[]{refByte}) + new String(a.getBases()); String newBases = new String(new byte[]{refByte}) + a.getBaseString();
alleles.add(Allele.create(newBases,a.isReference())); alleles.add(Allele.create(newBases,a.isReference()));
} }
@ -610,7 +610,7 @@ public class VariantContextUtils {
List<Allele> newGenotypeAlleles = new ArrayList<Allele>(); List<Allele> newGenotypeAlleles = new ArrayList<Allele>();
for (Allele a : inAlleles) { for (Allele a : inAlleles) {
if (a.isCalled()) { if (a.isCalled()) {
String newBases = new String(new byte[]{refByte}) + new String(a.getBases()); String newBases = new String(new byte[]{refByte}) + a.getBaseString();
newGenotypeAlleles.add(Allele.create(newBases,a.isReference())); newGenotypeAlleles.add(Allele.create(newBases,a.isReference()));
} }
else { else {

3
java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java
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@ -129,7 +129,6 @@ public class PickSequenomProbes extends RodWalker<String, String> {
RODRecordList snpList = snpMaskIterator.seekForward(GenomeLocParser.createGenomeLoc(contig,offset-200,offset+200)); RODRecordList snpList = snpMaskIterator.seekForward(GenomeLocParser.createGenomeLoc(contig,offset-200,offset+200));
if ( snpList != null && snpList.size() != 0 ) { if ( snpList != null && snpList.size() != 0 ) {
Iterator<GATKFeature> snpsInWindow = snpList.iterator(); Iterator<GATKFeature> snpsInWindow = snpList.iterator();
int i = 0;
while ( snpsInWindow.hasNext() ) { while ( snpsInWindow.hasNext() ) {
GenomeLoc snp = snpsInWindow.next().getLocation(); GenomeLoc snp = snpsInWindow.next().getLocation();
// we don't really want to mask out multi-base indels // we don't really want to mask out multi-base indels
@ -157,7 +156,7 @@ public class PickSequenomProbes extends RodWalker<String, String> {
else if ( vc.isInsertion() ) else if ( vc.isInsertion() )
assay_sequence = leading_bases + "[-/" + vc.getAlternateAllele(0).toString() + "]" + (char)ref.getBase() + trailing_bases; assay_sequence = leading_bases + "[-/" + vc.getAlternateAllele(0).toString() + "]" + (char)ref.getBase() + trailing_bases;
else if ( vc.isDeletion() ) else if ( vc.isDeletion() )
assay_sequence = leading_bases + "[" + new String(vc.getReference().getBases()) + "/-]" + trailing_bases.substring(vc.getReference().length()-1); assay_sequence = leading_bases + "[" + vc.getReference().getBaseString() + "/-]" + trailing_bases.substring(vc.getReference().length()-1);
else else
return ""; return "";

6
java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFWriter.java
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@ -140,7 +140,7 @@ public class VCFWriter {
// REF // REF
alleleMap.put(vc.getReference(), "0"); alleleMap.put(vc.getReference(), "0");
String refString = new String(vc.getReference().getBases()); String refString = vc.getReference().getBaseString();
mWriter.write(refString); mWriter.write(refString);
mWriter.write(VCFConstants.FIELD_SEPARATOR); mWriter.write(VCFConstants.FIELD_SEPARATOR);
@ -148,13 +148,13 @@ public class VCFWriter {
if ( vc.isVariant() ) { if ( vc.isVariant() ) {
Allele altAllele = vc.getAlternateAllele(0); Allele altAllele = vc.getAlternateAllele(0);
alleleMap.put(altAllele, "1"); alleleMap.put(altAllele, "1");
String alt = new String(altAllele.getBases()); String alt = altAllele.getBaseString();
mWriter.write(alt); mWriter.write(alt);
for (int i = 1; i < vc.getAlternateAlleles().size(); i++) { for (int i = 1; i < vc.getAlternateAlleles().size(); i++) {
altAllele = vc.getAlternateAllele(i); altAllele = vc.getAlternateAllele(i);
alleleMap.put(altAllele, String.valueOf(i+1)); alleleMap.put(altAllele, String.valueOf(i+1));
alt = new String(altAllele.getBases()); alt = altAllele.getBaseString();
mWriter.write(","); mWriter.write(",");
mWriter.write(alt); mWriter.write(alt);
} }