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Fix minor mapping quality bug. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1973 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-11-04 14:33:23 +00:00
parent 21b1ece45d
commit 43c3ee61d5
2 changed files with 5 additions and 2 deletions
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3
c/bwa/bwa_gateway.cpp
View File

@ -24,6 +24,9 @@ BWA::BWA(const char* ann_filename,
bwts[1] = bwt_restore_bwt(reverse_bwt_filename); bwts[1] = bwt_restore_bwt(reverse_bwt_filename);
bwt_restore_sa(reverse_sa_filename, bwts[1]); bwt_restore_sa(reverse_sa_filename, bwts[1]);
load_default_options(); load_default_options();
// initialize the bwase subsystem
bwase_initialize();
} }
BWA::~BWA() { BWA::~BWA() {

4
java/src/org/broadinstitute/sting/alignment/bwa/AlignmentValidationWalker.java
View File

@ -55,7 +55,7 @@ public class AlignmentValidationWalker extends ReadWalker<Integer,Integer> {
@Override @Override
public boolean filter(char[] ref, SAMRecord read) { public boolean filter(char[] ref, SAMRecord read) {
return true; 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<Integer,Integer> {
matches &= (alignment.getCigar().equals(read.getCigar())); matches &= (alignment.getCigar().equals(read.getCigar()));
int mapQDelta = Math.abs(alignment.getMappingQuality()-read.getMappingQuality()); int mapQDelta = Math.abs(alignment.getMappingQuality()-read.getMappingQuality());
maxMapQDelta = Math.max(mapQDelta,maxMapQDelta); maxMapQDelta = Math.max(mapQDelta,maxMapQDelta);
//matches &= (alignment.getMappingQuality() == read.getMappingQuality()); matches &= (alignment.getMappingQuality() == read.getMappingQuality());
if(matches) break; if(matches) break;
} }
} }