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As per Menachem's last commit, there's a minimally more efficient way of doing the MQ cap. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4782 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-12-03 16:37:08 +00:00
parent 92cf7744a6
commit ec174dc0ba
1 changed files with 5 additions and 4 deletions
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9
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
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@ -117,7 +117,10 @@ public class UnifiedGenotyperEngine {
}
private void initialize(GenomeAnalysisEngine toolkit, UnifiedArgumentCollection UAC, Logger logger, PrintStream verboseWriter, VariantAnnotatorEngine engine, int numSamples) {
this.UAC = UAC;
// note that, because we cap the base quality by the mapping quality, minMQ cannot be less than minBQ
this.UAC = UAC.clone();
this.UAC.MIN_MAPPING_QUALTY_SCORE = Math.max(UAC.MIN_MAPPING_QUALTY_SCORE, UAC.MIN_BASE_QUALTY_SCORE);
this.logger = logger;
this.verboseWriter = verboseWriter;
this.annotationEngine = engine;
@ -575,10 +578,8 @@ public class UnifiedGenotyperEngine {
// all bits are set to false by default
BitSet bitset = new BitSet(record.getReadLength());
// if the mapping quality is too low or the mate is bad, we can just zero out the whole read and continue.
// note that, because we cap the base quality by the mapping quality, if MQ < minBQ then we can filter this read.
// if the mapping quality is too low or the mate is bad, we can just zero out the whole read and continue
if ( record.getMappingQuality() < UAC.MIN_MAPPING_QUALTY_SCORE ||
record.getMappingQuality() < UAC.MIN_BASE_QUALTY_SCORE ||
(!UAC.USE_BADLY_MATED_READS && BadMateFilter.hasBadMate(record)) ) {
return bitset;
}