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RR bug: we need to test that the mapping and base quals are >= the MIN values and not just >. This was causing us to drop Q20 bases.

This commit is contained in:
Eric Banks 2012-09-22 21:32:29 -04:00
parent f6a22e5f50
commit 60b93acf7d
1 changed files with 2 additions and 2 deletions
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4
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
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@ -674,7 +674,7 @@ public class SlidingWindow {
// check if the read is either before or inside the variant region
if (read.getSoftStart() <= refStop) {
// check if the read is inside the variant region
if (read.getMappingQuality() > MIN_MAPPING_QUALITY && read.getSoftEnd() >= refStart) {
if (read.getMappingQuality() >= MIN_MAPPING_QUALITY && read.getSoftEnd() >= refStart) {
// check if the read contains the het site
if (read.getSoftStart() <= hetRefPosition && read.getSoftEnd() >= hetRefPosition) {
int readPos = ReadUtils.getReadCoordinateForReferenceCoordinate(read, hetRefPosition, ReadUtils.ClippingTail.LEFT_TAIL);
@ -682,7 +682,7 @@ public class SlidingWindow {
byte qual = read.getBaseQualities(EventType.BASE_SUBSTITUTION)[readPos];
// check if base passes the filters!
if (qual > MIN_BASE_QUAL_TO_COUNT) {
if (qual >= MIN_BASE_QUAL_TO_COUNT) {
// check which haplotype this read represents and take the index of it from the list of headers
if (haplotypeHeaderMap.containsKey(base)) {
haplotype = haplotypeHeaderMap.get(base);