zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Reduced header to single sample when useSingleSample arg is given (to prevent lots of pointless no-calls) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4588 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
fromer 2010-10-27 23:02:10 +00:00
parent 34538bf2b3
commit 15183ed778
2 changed files with 9 additions and 0 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

6
java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergePhasedSegregatingAlternateAllelesVCFWriter.java
View File

@ -88,6 +88,12 @@ public class MergePhasedSegregatingAlternateAllelesVCFWriter implements VCFWrite
}
public void writeHeader(VCFHeader header) {
if (useSingleSample != null) { // only want to output context for one sample
Set<String> singSampSet = new TreeSet<String>();
singSampSet.add(useSingleSample);
header = new VCFHeader(header.getMetaData(), singSampSet);
}
innerWriter.writeHeader(header);
}

3
java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java
View File

@ -144,6 +144,9 @@ public class MergeSegregatingAlternateAllelesWalker extends RodWalker<Integer, I
public void onTraversalDone(Integer result) {
vcMergerWriter.close();
if (useSingleSample != null)
System.out.println("Only considered single sample: " + useSingleSample);
System.out.println("Number of successive pairs of records (any distance): " + vcMergerWriter.getNumRecordsAttemptToMerge());
System.out.println("Number of potentially merged records (distance <= " + maxGenomicDistanceForMNP + "): " + vcMergerWriter.getNumRecordsWithinDistance());
System.out.println("Number of records merged [all samples are mergeable, some sample has a MNP of ALT alleles]: " + vcMergerWriter.getNumMergedRecords());