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Fixing merge conflicts related to the comment formatting in the BQSR.

This commit is contained in:
Ryan Poplin 2012-10-10 16:03:58 -04:00
parent 40a3b5bfe2 45717349dc
commit 08b8ce6903
1 changed files with 1 additions and 1 deletions
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public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
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@ -230,7 +230,7 @@ public class BaseRecalibrator extends LocusWalker<Long, Long> implements TreeRed
final int offset = p.getOffset(); final int offset = p.getOffset();
// This read has been marked to be skipped or base is low quality (we don't recalibrate low quality bases) // This read has been marked to be skipped or base is low quality (we don't recalibrate low quality bases)
if (readHasBeenSkipped(read) || isLowQualityBase(p)) if (readHasBeenSkipped(read) || p.isInsertionAtBeginningOfRead() || isLowQualityBase(p) )
continue; continue;
if (readNotSeen(read)) { if (readNotSeen(read)) {