From 43c3ee61d5f982367bc006fda5d69b73505c5591 Mon Sep 17 00:00:00 2001 From: hanna Date: Wed, 4 Nov 2009 14:33:23 +0000 Subject: [PATCH] Fix minor mapping quality bug. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1973 348d0f76-0448-11de-a6fe-93d51630548a --- c/bwa/bwa_gateway.cpp | 3 +++ .../sting/alignment/bwa/AlignmentValidationWalker.java | 4 ++-- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/c/bwa/bwa_gateway.cpp b/c/bwa/bwa_gateway.cpp index a5fb045ec..d73d4ef86 100644 --- a/c/bwa/bwa_gateway.cpp +++ b/c/bwa/bwa_gateway.cpp @@ -24,6 +24,9 @@ BWA::BWA(const char* ann_filename, bwts[1] = bwt_restore_bwt(reverse_bwt_filename); bwt_restore_sa(reverse_sa_filename, bwts[1]); load_default_options(); + + // initialize the bwase subsystem + bwase_initialize(); } BWA::~BWA() { diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/AlignmentValidationWalker.java b/java/src/org/broadinstitute/sting/alignment/bwa/AlignmentValidationWalker.java index 50cba3151..143f0a073 100644 --- a/java/src/org/broadinstitute/sting/alignment/bwa/AlignmentValidationWalker.java +++ b/java/src/org/broadinstitute/sting/alignment/bwa/AlignmentValidationWalker.java @@ -55,7 +55,7 @@ public class AlignmentValidationWalker extends ReadWalker { @Override public boolean filter(char[] ref, SAMRecord read) { return true; - //return read.getReadName().contains("SL-XBC:1:76:604:397#0"); + //return read.getReadName().contains("SL-XBC:1:61:1719:1512#0"); } /** @@ -84,7 +84,7 @@ public class AlignmentValidationWalker extends ReadWalker { matches &= (alignment.getCigar().equals(read.getCigar())); int mapQDelta = Math.abs(alignment.getMappingQuality()-read.getMappingQuality()); maxMapQDelta = Math.max(mapQDelta,maxMapQDelta); - //matches &= (alignment.getMappingQuality() == read.getMappingQuality()); + matches &= (alignment.getMappingQuality() == read.getMappingQuality()); if(matches) break; } }