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Handles bam pileups where some of the reads have SQ tags and some don't. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@958 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-06-10 08:17:15 +00:00
parent 36c98b9d6c
commit 2b0e7f612b
1 changed files with 1 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/utils/BasicPileup.java
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@ -98,7 +98,7 @@ abstract public class BasicPileup implements Pileup {
byte[] compressedQuals = (byte[]) read.getAttribute("SQ"); byte[] compressedQuals = (byte[]) read.getAttribute("SQ");
byte base2; byte base2;
//byte qual2; //byte qual2;
if (compressedQuals != null) { if (compressedQuals != null && compressedQuals.length == read.getReadLength()) {
base2 = (byte) BaseUtils.baseIndexToSimpleBase(QualityUtils.compressedQualityToBaseIndex(compressedQuals[offset])); base2 = (byte) BaseUtils.baseIndexToSimpleBase(QualityUtils.compressedQualityToBaseIndex(compressedQuals[offset]));
//qual2 = QualityUtils.probToQual(QualityUtils.compressedQualityToProb(compressedQuals[offset])); //qual2 = QualityUtils.probToQual(QualityUtils.compressedQualityToProb(compressedQuals[offset]));
hasAtLeastOneSQField = true; hasAtLeastOneSQField = true;