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Modified PowerBelowFrequency to ignore reads below a user-defined mapping quality. Request from Jason Flannick. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1813 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2009-10-12 20:59:24 +00:00
parent ec68ae3bc5
commit ecbb11e017
1 changed files with 8 additions and 0 deletions
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8
java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/PowerBelowFrequencyWalker.java
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@ -41,6 +41,9 @@ public class PowerBelowFrequencyWalker extends LocusWalker<Integer,Integer> {
@Argument(fullName="useMeanProb", doc="Use the mean probability as the \"average quality\" rather than median Q-score")
boolean useMean = false;
@Argument(fullName="minimumMappingQuality", shortName="mmq", doc="Only use reads above this mapping quality in the power calculation", required=false)
int minMappingQuality = -1;
public void initialize() {
if ( alleleFreq < 1 ) {
String err = "Allele frequency (-af) must be greater than or equal to one.";
@ -67,6 +70,11 @@ public class PowerBelowFrequencyWalker extends LocusWalker<Integer,Integer> {
context = new AlignmentContext(context.getLocation(), thresh.getFirst(), thresh.getSecond());
}
if ( minMappingQuality > -1 ) {
Pair<List<SAMRecord>,List<Integer>> goodMaps = PoolUtils.thresholdReadsByMappingQuality(context.getReads(),context.getOffsets(),minMappingQuality);
context = new AlignmentContext(context.getLocation(), goodMaps.getFirst(), goodMaps.getSecond());
}
// calculate powers and put into output string
for ( int i = 1; i <= alleleFreq; i ++ ) {