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Fix the stats coming out of FlagStat. I will add an integration test in unstable

This commit is contained in:
Eric Banks 2012-04-10 22:26:10 -04:00
parent bb1dff4ea4
commit f46f7d0590
1 changed files with 12 additions and 12 deletions
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24
public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStatWalker.java
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@ -127,7 +127,7 @@ public class FlagStatWalker extends ReadWalker<Integer, Integer> {
if (read.getDuplicateReadFlag()) {
myStat.duplicates++;
}
if (read.getReferenceIndex() >= 0) {
if (!read.getReadUnmappedFlag()) {
myStat.mapped++;
}
if (read.getReadPairedFlag()) {
@ -139,21 +139,21 @@ public class FlagStatWalker extends ReadWalker<Integer, Integer> {
myStat.read1++;
}
if (read.getProperPairFlag()) {
myStat.properly_paired++;
}
if (!read.getMateUnmappedFlag() && read.getReferenceIndex() >= 0) {
if (!read.getReadUnmappedFlag() && !read.getMateUnmappedFlag()) {
myStat.with_itself_and_mate_mapped++;
}
if (read.getMateUnmappedFlag()) {
myStat.singletons++;
}
}
if (read.getReferenceIndex() >= 0 && read.getMateReferenceIndex() >= 0 && ! read.getReferenceIndex().equals(read.getMateReferenceIndex())) {
myStat.with_mate_mapped_to_a_different_chr++;
if (read.getMappingQuality() >= 5) {
myStat.with_mate_mapped_to_a_different_chr_maq_greaterequal_than_5++;
if (!read.getReferenceIndex().equals(read.getMateReferenceIndex())) {
myStat.with_mate_mapped_to_a_different_chr++;
if (read.getMappingQuality() >= 5) {
myStat.with_mate_mapped_to_a_different_chr_maq_greaterequal_than_5++;
}
}
}
if (!read.getReadUnmappedFlag() && read.getMateUnmappedFlag()) {
myStat.singletons++;
}
}
return 1;