/** * Determines whether a paired of SAMRecord matches this filter * * @param first the first SAMRecord to evaluate * @param second the second SAMRecord to evaluate * * @return true if the SAMRecords matches the filter, otherwise false */ public boolean filterOut(final SAMRecord first, final SAMRecord second) { // if either fails, exclude them both return (filterOut(first) || filterOut(second)); } }
/** * Writes the binary fastq file(s) to the output directory */ public void writeBfqFiles() { final SamReader reader = SamReaderFactory.makeDefault().open(bamFile); final Iterator<SAMRecord> iterator = reader.iterator(); // Filter out noise reads and reads that fail the quality filter final TagFilter tagFilter = new TagFilter(ReservedTagConstants.XN, 1); final FailsVendorReadQualityFilter qualityFilter = new FailsVendorReadQualityFilter(); final WholeReadClippedFilter clippedFilter = new WholeReadClippedFilter(); if (!pairedReads) { List<SamRecordFilter> filters = new ArrayList<SamRecordFilter>(); filters.add(tagFilter); filters.add(clippedFilter); if (!this.includeNonPfReads) { filters.add(qualityFilter); } writeSingleEndBfqs(iterator, filters); codec1.close(); } else { writePairedEndBfqs(iterator, tagFilter, qualityFilter, clippedFilter); codec1.close(); codec2.close(); } log.info("Wrote " + wrote + " bfq records."); CloserUtil.close(reader); }
/** * Writes the binary fastq file(s) to the output directory */ public void writeBfqFiles() { final SamReader reader = SamReaderFactory.makeDefault().open(bamFile); final Iterator<SAMRecord> iterator = reader.iterator(); // Filter out noise reads and reads that fail the quality filter final TagFilter tagFilter = new TagFilter(ReservedTagConstants.XN, 1); final FailsVendorReadQualityFilter qualityFilter = new FailsVendorReadQualityFilter(); final WholeReadClippedFilter clippedFilter = new WholeReadClippedFilter(); if (!pairedReads) { List<SamRecordFilter> filters = new ArrayList<SamRecordFilter>(); filters.add(tagFilter); filters.add(clippedFilter); if (!this.includeNonPfReads) { filters.add(qualityFilter); } writeSingleEndBfqs(iterator, filters); codec1.close(); } else { writePairedEndBfqs(iterator, tagFilter, qualityFilter, clippedFilter); codec1.close(); codec2.close(); } log.info("Wrote " + wrote + " bfq records."); CloserUtil.close(reader); }
/** * Determines whether a paired of SAMRecord matches this filter * * @param first the first SAMRecord to evaluate * @param second the second SAMRecord to evaluate * * @return true if the SAMRecords matches the filter, otherwise false */ @Override public boolean filterOut(final SAMRecord first, final SAMRecord second) { // if either fails, exclude them both return (filterOut(first) || filterOut(second)); } }
/** * Determines whether a paired of SAMRecord matches this filter * * @param first the first SAMRecord to evaluate * @param second the second SAMRecord to evaluate * * @return true if the SAMRecords matches the filter, otherwise false */ @Override public boolean filterOut(final SAMRecord first, final SAMRecord second) { // if either fails, exclude them both return (filterOut(first) || filterOut(second)); } }