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Fixing a bug when breaking up active regions where the resulting regions would overlap by one base. Adding quality score manipulation from the UG into the haplotype caller (qual capped by mapping quality, min qual threshold).

This commit is contained in:
Ryan Poplin 2012-04-20 14:02:55 -04:00
parent 1ea4e48a27
commit a57295eb75
2 changed files with 3 additions and 3 deletions
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4
public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java
View File

@ -158,11 +158,11 @@ public class ActivityProfile {
// find the best place to break up the large active region
Double minProb = Double.MAX_VALUE;
int cutPoint = -1;
for( int iii = curStart + 45; iii < curEnd - 45; iii++ ) { // BUGBUG: assumes maxRegionSize >> 45
for( int iii = curStart + 50; iii < curEnd - 50; iii++ ) { // BUGBUG: assumes maxRegionSize >> 50
if( isActiveList.get(iii) < minProb ) { minProb = isActiveList.get(iii); cutPoint = iii; }
}
final List<ActiveRegion> leftList = createActiveRegion(isActive, curStart, cutPoint, activeRegionExtension, maxRegionSize, new ArrayList<ActiveRegion>());
final List<ActiveRegion> rightList = createActiveRegion(isActive, cutPoint, curEnd, activeRegionExtension, maxRegionSize, new ArrayList<ActiveRegion>());
final List<ActiveRegion> rightList = createActiveRegion(isActive, cutPoint+1, curEnd, activeRegionExtension, maxRegionSize, new ArrayList<ActiveRegion>());
returnList.addAll( leftList );
returnList.addAll( rightList );
return returnList;

2
public/java/test/org/broadinstitute/sting/gatk/walkers/activeregionqc/CountReadsInActiveRegionsIntegrationTest.java
View File

@ -38,7 +38,7 @@ public class CountReadsInActiveRegionsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T CountReadsInActiveRegions -R " + b37KGReference + " -I " + b37GoodNA12878BAM + " -L 20:10,000,000-10,200,000 -o %s",
1,
Arrays.asList("1e9e8d637d2acde23fa99fe9dc07e3e2"));
Arrays.asList("942d067e6863a3f3524f67dc0aa02ef2"));
executeTest("CountReadsInActiveRegions:", spec);
}
}