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Some quick and dirty fixes to support querying unmapped BAM files. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1228 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-07-14 01:25:20 +00:00
parent e4152af387
commit bfe90af5e2
2 changed files with 23 additions and 1 deletions
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12
java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java
View File

@ -177,6 +177,10 @@ public class SAMDataSource implements SimpleDataSource {
private StingSAMIterator seekRead( ReadShard shard ) throws SimpleDataSourceLoadException {
StingSAMIterator iter = null;
// If there are no entries in the sequence dictionary, there can't possibly be any unmapped reads. Force state to 'unmapped'.
if( isSequenceDictionaryEmpty() )
intoUnmappedReads = true;
if (!intoUnmappedReads) {
if (lastReadPos == null) {
lastReadPos = GenomeLocParser.createGenomeLoc(getHeader().getSequenceDictionary().getSequence(0).getSequenceIndex(), 0, Integer.MAX_VALUE);
@ -312,6 +316,14 @@ public class SAMDataSource implements SimpleDataSource {
return bound;
}
/**
* Determines whether the BAM file is completely unsequenced. Requires that the resource pool be initialized.
* @return True if the sequence dictionary is completely empty. False otherwise.
*/
private boolean isSequenceDictionaryEmpty() {
return getHeader().getSequenceDictionary().isEmpty();
}
/**
* Even though the iterator has seeked to the correct location, there may be multiple reads at that location,
* and we may have given some of them out already. Move the iterator to the correct location using the readsAtLastPos variable

12
java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
View File

@ -154,7 +154,17 @@ public class MergingSamRecordIterator2 implements CloseableIterator<SAMRecord>,
}
final SAMRecordComparator comparator = getComparator();
for (final SAMFileReader reader : samHeaderMerger.getReaders()) {
Iterator<SAMRecord> recordIter = reader.queryUnmapped();
Iterator<SAMRecord> recordIter = null;
if( reader.hasIndex() ) {
recordIter = reader.queryUnmapped();
}
else {
// HACK: Supporting completely unmapped BAM files is easy. Let's do a quick check to make sure
// these BAMs aren't partially indexed.
if( reader.getFileHeader().getSequenceDictionary().size() > 0 )
throw new StingException("Partially mapped BAM files without indices are not supported");
recordIter = reader.iterator();
}
final ComparableSamRecordIterator iterator = new ComparableSamRecordIterator(reader, recordIter, comparator);
addIfNotEmpty(iterator);
}