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

Fix bug in the interval sharder in cases where contigs specified in intervals are not present in any supplied BAM file. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3268 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-04-28 20:42:04 +00:00
parent b648e89096
commit 4617abf1ff
1 changed files with 6 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

7
java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalSharder.java
View File

@ -105,6 +105,8 @@ public class IntervalSharder {
BinMergingIterator binMerger = new BinMergingIterator();
for(SAMReaderID id: dataSource.getReaderIDs()) {
final SAMSequenceRecord referenceSequence = dataSource.getHeader(id).getSequence(contig);
if(referenceSequence == null)
continue;
final CachingBAMFileIndex index = dataSource.getIndex(id);
binMerger.addReader(id,
index,
@ -119,6 +121,9 @@ public class IntervalSharder {
if(!location.getContig().equals(contig))
throw new StingException("Location outside bounds of contig");
if(!binIterator.hasNext())
break;
int locationStart = (int)location.getStart();
final int locationStop = (int)location.getStop();
@ -195,7 +200,7 @@ public class IntervalSharder {
filePointers.add(lastFilePointer);
// Lookup the locations for every file pointer in the index.
for(SAMReaderID id: dataSource.getReaderIDs()) {
for(SAMReaderID id: readerToIndexMap.keySet()) {
CachingBAMFileIndex index = readerToIndexMap.get(id);
for(FilePointer filePointer: filePointers)
filePointer.addFileSpans(id,index.getChunksOverlapping(filePointer.overlap.getBin(id)));