/** write out any references between the currentReference and the nextReference */
private void advanceToReference(final int nextReference) {
while (currentReference < nextReference) {
final BAMIndexContent content = indexBuilder.processReference(currentReference);
outputWriter.writeReference(content);
currentReference++;
if (currentReference < numReferences) {
indexBuilder.startNewReference();
}
}
}
/**
* Record any index information for a given BAM record. If this alignment starts a new reference,
* write out the old reference. Requires a non-null value for rec.getFileSource().
*
* @param rec The BAM record
*/
public void processAlignment(final SAMRecord rec) {
try {
final int reference = rec.getReferenceIndex();
if (reference != SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX && reference != currentReference) {
// process any completed references
advanceToReference(reference);
}
indexBuilder.processAlignment(rec);
} catch (final Exception e) {
throw new SAMException("Exception creating BAM index for record " + rec, e);
}
}
/**
* After all the alignment records have been processed, finish is called. Writes any final
* information and closes the output file.
*/
public void finish() {
// process any remaining references
advanceToReference(numReferences);
outputWriter.writeNoCoordinateRecordCount(indexBuilder.getNoCoordinateRecordCount());
outputWriter.close();
}
