From 0eeb659aa3b24e64061f2071e68d2d16c89b59b5 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 9 Aug 2010 20:35:56 +0000
Subject: [PATCH] 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
---
 .../gatk/contexts/variantcontext/VariantContextUtils.java   | 4 ++--
 .../sting/gatk/walkers/sequenom/PickSequenomProbes.java     | 3 +--
 .../broadinstitute/sting/utils/genotype/vcf/VCFWriter.java  | 6 +++---
 3 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
index 51029e8e0..a094707a1 100755
--- a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
+++ b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
@@ -598,7 +598,7 @@ public class VariantContextUtils {
 
             for (Allele a : inputVC.getAlleles()) {
                 // 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()));
             }
 
@@ -610,7 +610,7 @@ public class VariantContextUtils {
                 List<Allele> newGenotypeAlleles = new ArrayList<Allele>();
                 for (Allele a : inAlleles) {
                     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()));
                     }
                     else {
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java b/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java
index 92fe1a97e..28ac7123e 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java
@@ -129,7 +129,6 @@ public class PickSequenomProbes extends RodWalker<String, String> {
             RODRecordList snpList =  snpMaskIterator.seekForward(GenomeLocParser.createGenomeLoc(contig,offset-200,offset+200));
             if ( snpList != null && snpList.size() != 0 ) {
                 Iterator<GATKFeature>  snpsInWindow = snpList.iterator();
-                int i = 0;
                 while ( snpsInWindow.hasNext() ) {
                     GenomeLoc snp = snpsInWindow.next().getLocation();
                     // 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() )
             assay_sequence = leading_bases + "[-/" + vc.getAlternateAllele(0).toString() + "]" + (char)ref.getBase() + trailing_bases;
         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
             return "";
 
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFWriter.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFWriter.java
index d3e4b7861..a2cbcf2aa 100644
--- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFWriter.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFWriter.java
@@ -140,7 +140,7 @@ public class VCFWriter {
 
             // REF
             alleleMap.put(vc.getReference(), "0");
-            String refString = new String(vc.getReference().getBases());
+            String refString = vc.getReference().getBaseString();
             mWriter.write(refString);
             mWriter.write(VCFConstants.FIELD_SEPARATOR);
 
@@ -148,13 +148,13 @@ public class VCFWriter {
             if ( vc.isVariant() ) {
                 Allele altAllele = vc.getAlternateAllele(0);
                 alleleMap.put(altAllele, "1");
-                String alt = new String(altAllele.getBases());
+                String alt = altAllele.getBaseString();
                 mWriter.write(alt);
 
                 for (int i = 1; i < vc.getAlternateAlleles().size(); i++) {
                     altAllele = vc.getAlternateAllele(i);
                     alleleMap.put(altAllele, String.valueOf(i+1));
-                    alt = new String(altAllele.getBases());
+                    alt = altAllele.getBaseString();
                     mWriter.write(",");
                     mWriter.write(alt);
                 }