/**
* Record any index information for a given BAM record
*
* @param rec The BAM record. Requires rec.getFileSource() is non-null.
*/
public void processAlignment(final SAMRecord rec) {
// metadata
indexStats.recordMetaData(rec);
if (rec.getAlignmentStart() == SAMRecord.NO_ALIGNMENT_START) {
return; // do nothing for records without coordinates, but count them
}
// various checks
final int reference = rec.getReferenceIndex();
if (reference != currentReference) {
throw new SAMException(
"Unexpected reference "
+ reference
+ " when constructing index for "
+ currentReference
+ " for record "
+ rec);
}
binningIndexBuilder.processFeature(
new BinningIndexBuilder.FeatureToBeIndexed() {
@Override
public int getStart() {
return rec.getAlignmentStart();
}
@Override
public int getEnd() {
return rec.getAlignmentEnd();
}
@Override
public Integer getIndexingBin() {
final Integer binNumber = rec.getIndexingBin();
return (binNumber == null ? rec.computeIndexingBin() : binNumber);
}
@Override
public Chunk getChunk() {
final SAMFileSource source = rec.getFileSource();
if (source == null) {
throw new SAMException(
"No source (virtual file offsets); needed for indexing on BAM Record " + rec);
}
return ((BAMFileSpan) source.getFilePointer()).getSingleChunk();
}
});
}
/**
* Creates the BAMIndexContent for this reference. Requires all alignments of the reference have
* already been processed.
*
* @return Null if there are no features for this reference.
*/
public BAMIndexContent processReference(final int reference) {
if (reference != currentReference) {
throw new SAMException(
"Unexpected reference "
+ reference
+ " when constructing index for "
+ currentReference);
}
final BinningIndexContent indexContent = binningIndexBuilder.generateIndexContent();
if (indexContent == null) return null;
return new BAMIndexContent(
indexContent.getReferenceSequence(),
indexContent.getBins(),
indexStats,
indexContent.getLinearIndex());
}