/** * 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); } }
/** * 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); } }
/** * 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); } }