private void filterReads(final FilteringSamIterator filteringIterator) { // get OUTPUT header from INPUT and overwrite it if necessary final SAMFileHeader fileHeader = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).getFileHeader(INPUT); final SAMFileHeader.SortOrder inputSortOrder = fileHeader.getSortOrder(); if (SORT_ORDER != null) { fileHeader.setSortOrder(SORT_ORDER); } if (FILTER == Filter.includePairedIntervals && fileHeader.getSortOrder() != SAMFileHeader.SortOrder.coordinate) { throw new UnsupportedOperationException("Input must be coordinate sorted to use includePairedIntervals"); } final boolean presorted = inputSortOrder.equals(fileHeader.getSortOrder()); log.info("Filtering [presorted=" + presorted + "] " + INPUT.getName() + " -> OUTPUT=" + OUTPUT.getName() + " [sortorder=" + fileHeader.getSortOrder().name() + "]"); // create OUTPUT file final SAMFileWriter outputWriter = new SAMFileWriterFactory().makeSAMOrBAMWriter(fileHeader, presorted, OUTPUT); final ProgressLogger progress = new ProgressLogger(log, (int) 1e6, "Written"); while (filteringIterator.hasNext()) { final SAMRecord rec = filteringIterator.next(); outputWriter.addAlignment(rec); progress.record(rec); } filteringIterator.close(); outputWriter.close(); log.info(new DecimalFormat("#,###").format(progress.getCount()) + " SAMRecords written to " + OUTPUT.getName()); }
private void filterReads(final FilteringSamIterator filteringIterator) { // get OUTPUT header from INPUT and overwrite it if necessary final SAMFileHeader fileHeader = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).getFileHeader(INPUT); final SAMFileHeader.SortOrder inputSortOrder = fileHeader.getSortOrder(); if (SORT_ORDER != null) { fileHeader.setSortOrder(SORT_ORDER); } if (FILTER == Filter.includePairedIntervals && fileHeader.getSortOrder() != SAMFileHeader.SortOrder.coordinate) { throw new UnsupportedOperationException("Input must be coordinate sorted to use includePairedIntervals"); } final boolean presorted = inputSortOrder.equals(fileHeader.getSortOrder()); log.info("Filtering [presorted=" + presorted + "] " + INPUT.getName() + " -> OUTPUT=" + OUTPUT.getName() + " [sortorder=" + fileHeader.getSortOrder().name() + "]"); // create OUTPUT file final SAMFileWriter outputWriter = new SAMFileWriterFactory().makeSAMOrBAMWriter(fileHeader, presorted, OUTPUT); final ProgressLogger progress = new ProgressLogger(log, (int) 1e6, "Written"); while (filteringIterator.hasNext()) { final SAMRecord rec = filteringIterator.next(); outputWriter.addAlignment(rec); progress.record(rec); } filteringIterator.close(); outputWriter.close(); log.info(new DecimalFormat("#,###").format(progress.getCount()) + " SAMRecords written to " + OUTPUT.getName()); }
/** * Path for writing bfqs for single-end reads * * @param iterator the iterator with he SAM Records to write * @param filters the list of filters to be applied */ private void writeSingleEndBfqs(final Iterator<SAMRecord> iterator, final List<SamRecordFilter> filters) { // Open the codecs for writing int fileIndex = 0; initializeNextBfqFiles(fileIndex++); int records = 0; final FilteringSamIterator it = new FilteringSamIterator(iterator, new AggregateFilter(filters)); while (it.hasNext()) { final SAMRecord record = it.next(); records++; if (records % increment == 0) { record.setReadName(record.getReadName() + "/1"); writeFastqRecord(codec1, record); wrote++; if (wrote % 1000000 == 0) { log.info(wrote + " records processed."); } if (chunk > 0 && wrote % chunk == 0) { initializeNextBfqFiles(fileIndex++); } } } }
/** * Path for writing bfqs for single-end reads * * @param iterator the iterator with he SAM Records to write * @param filters the list of filters to be applied */ private void writeSingleEndBfqs(final Iterator<SAMRecord> iterator, final List<SamRecordFilter> filters) { // Open the codecs for writing int fileIndex = 0; initializeNextBfqFiles(fileIndex++); int records = 0; final FilteringSamIterator it = new FilteringSamIterator(iterator, new AggregateFilter(filters)); while (it.hasNext()) { final SAMRecord record = it.next(); records++; if (records % increment == 0) { record.setReadName(record.getReadName() + "/1"); writeFastqRecord(codec1, record); wrote++; if (wrote % 1000000 == 0) { log.info(wrote + " records processed."); } if (chunk > 0 && wrote % chunk == 0) { initializeNextBfqFiles(fileIndex++); } } } }
itr.next(); count++;
itr.next(); count++;