From 982c47bfa7ce48e2d4d53a445cff958212354ab0 Mon Sep 17 00:00:00 2001 From: Christopher Hartl Date: Thu, 22 Sep 2011 10:58:26 -0400 Subject: [PATCH 1/2] Remove duplicate effort in ReadUtils (with apologies to Mauricio) Big (but not major) cleanup of code in ILG - mostly excising the old likelihood model Activated the early-abort check for ILG. I think it should be better this way. --- .../java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java | 3 --- 1 file changed, 3 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java index 60c9c1780..c328bbc5a 100755 --- a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java @@ -681,9 +681,6 @@ public class ReadUtils { @Ensures({"result >= read.getUnclippedStart()", "result <= read.getUnclippedEnd() || readIsEntirelyInsertion(read)"}) public static int getRefCoordSoftUnclippedEnd(SAMRecord read) { - if ( read.getCigar().numCigarElements() == 1 && read.getCigar().getCigarElement(0).getOperator().equals(CigarOperator.INSERTION)) { - return read.getUnclippedEnd(); - } int stop = read.getUnclippedStart(); if (readIsEntirelyInsertion(read))