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Added count of number of mergeable records (within specified distance cutoff) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4560 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
fromer 2010-10-22 20:11:15 +00:00
parent 84b6d2926b
commit f06f955e06
2 changed files with 8 additions and 0 deletions
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7
java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergePhasedSegregatingPolymorphismsToMNPvcfWriter.java
View File

@ -46,6 +46,7 @@ public class MergePhasedSegregatingPolymorphismsToMNPvcfWriter implements VCFWri
private VCFRecord vcfrWaitingToMerge;
private List<VCFRecord> filteredVcfrList;
private int numRecordsWithinDistance;
private int numMergedRecords;
private Logger logger;
@ -59,6 +60,7 @@ public class MergePhasedSegregatingPolymorphismsToMNPvcfWriter implements VCFWri
this.maxGenomicDistanceForMNP = maxGenomicDistanceForMNP;
this.vcfrWaitingToMerge = null;
this.filteredVcfrList = new LinkedList<VCFRecord>();
this.numRecordsWithinDistance = 0;
this.numMergedRecords = 0;
this.logger = logger;
this.takeOwnershipOfInner = takeOwnershipOfInner;
@ -108,6 +110,7 @@ public class MergePhasedSegregatingPolymorphismsToMNPvcfWriter implements VCFWri
else { // waiting to merge vcfrWaitingToMerge, and curVcIsNotFiltered. So, attempt to merge them:
boolean mergedRecords = false;
if (minDistance(vcfrWaitingToMerge.vc, vc) <= maxGenomicDistanceForMNP) {
numRecordsWithinDistance++;
VariantContext mergedVc = VariantContextUtils.mergeIntoMNP(vcfrWaitingToMerge.vc, vc, referenceFileForMNPmerging);
if (mergedVc != null) {
mergedRecords = true;
@ -139,6 +142,10 @@ public class MergePhasedSegregatingPolymorphismsToMNPvcfWriter implements VCFWri
filteredVcfrList.clear();
}
public int getNumMergeableRecordsWithinDistance() {
return numRecordsWithinDistance;
}
public int getNumMergedRecords() {
return numMergedRecords;
}

1
java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingPolymorphismsWalker.java
View File

@ -134,6 +134,7 @@ public class MergeSegregatingPolymorphismsWalker extends RodWalker<Integer, Inte
*/
public void onTraversalDone(Integer result) {
vcMergerWriter.close();
System.out.println("Number of potentially merged records (distance <= "+ maxGenomicDistanceForMNP + "): " + vcMergerWriter.getNumMergeableRecordsWithinDistance());
System.out.println("Number of records merged: " + vcMergerWriter.getNumMergedRecords());
}
}