final Object testValue = commonTestValues[commonValuesIndex][3]; final TagFilter filter = new TagFilter(tag, validValues, includeReads); final SAMRecordSetBuilder builder = new SAMRecordSetBuilder(); builder.addPair("Paired", 1, 100, 200); Assert.assertEquals(filter.filterOut(record1), firstReadExpectedResult, testModule + " - " + testName); Assert.assertEquals(filter.filterOut(record1, record2), pairedExpectedResult, testModule + " - " + testName);
/** * 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); }
filters.add(new TagFilter(ReservedTagConstants.XN, 1)); if (!this.includeNonPfReads) { filters.add(new FailsVendorReadQualityFilter());
filters.add(new TagFilter(ReservedTagConstants.XN, 1)); if (!this.includeNonPfReads) { filters.add(new FailsVendorReadQualityFilter());