From 8b2c2e677bf61108d47891f1152db1e7ddd43a5b Mon Sep 17 00:00:00 2001 From: depristo Date: Tue, 14 Apr 2009 00:55:43 +0000 Subject: [PATCH] Uses the cleaner new GenomeLoc(read) syntax git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@396 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/iterators/LocusIteratorByHanger.java | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByHanger.java b/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByHanger.java index 0e361f193..10280356b 100755 --- a/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByHanger.java +++ b/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByHanger.java @@ -113,7 +113,8 @@ public class LocusIteratorByHanger extends LocusIterator { } protected void hangRead(final SAMRecord read) { - GenomeLoc readLoc = new GenomeLoc(read.getReferenceIndex(), read.getAlignmentStart()); + //GenomeLoc readLoc = new GenomeLoc(read.getReferenceIndex(), read.getAlignmentStart()); + GenomeLoc readLoc = new GenomeLoc(read); //System.out.printf("Adding read %s at %d%n", read.getReadName(), read.getAlignmentStart()); /* @@ -155,7 +156,7 @@ public class LocusIteratorByHanger extends LocusIterator { return true; else { final SAMRecord read = it.peek(); - GenomeLoc readLoc = GenomeLoc.genomicLocationOf(read); + GenomeLoc readLoc = new GenomeLoc(read); final boolean coveredP = currentPositionIsFullyCovered(readLoc); //System.out.printf("CoverP = %s => %b%n", readLoc, coveredP); return coveredP; @@ -177,7 +178,7 @@ public class LocusIteratorByHanger extends LocusIterator { SAMRecord read = it.next(); justCleared = false; - GenomeLoc readLoc = GenomeLoc.genomicLocationOf(read); + GenomeLoc readLoc = new GenomeLoc(read); if ( DEBUG ) { logger.debug(String.format(" Expanding window sizes %d with %d : left=%s, right=%s, readLoc = %s, cmp=%d%n", readHanger.size(), incrementSize,