Examples with SAMFileWriterFactory htsjdk.samtools.SAMFileWriterFactory used on opensource projects

Example 1 with SAMFileWriterFactory

use of htsjdk.samtools.SAMFileWriterFactory in project gatk by broadinstitute.

the class SplitReads method createWriters.

/**
     * Creates SAMFileWriter instances for the reader splitters based on the input file.
     * @param splitters Reader splitters.
     * @return A map of file name keys to SAMFileWriter.
     */
private Map<String, SAMFileGATKReadWriter> createWriters(final List<ReaderSplitter<?>> splitters) {
    final Map<String, SAMFileGATKReadWriter> outs = new LinkedHashMap<>();
    final SAMFileWriterFactory samFileWriterFactory = new SAMFileWriterFactory();
    final SAMFileHeader samFileHeaderIn = getHeaderForReads();
    // Build up a list of key options at each level.
    final List<List<?>> splitKeys = splitters.stream().map(splitter -> splitter.getSplitsBy(samFileHeaderIn)).collect(Collectors.toList());
    // For every combination of keys, add a SAMFileWriter.
    addKey(splitKeys, 0, "", key -> {
        outs.put(key, prepareSAMFileWriter(samFileWriterFactory, samFileHeaderIn, key));
    });
    return outs;
}

Example 2 with SAMFileWriterFactory

use of htsjdk.samtools.SAMFileWriterFactory in project gatk by broadinstitute.

the class SplitReads method createUnknownOutOnDemand.

// Create an output stream on demand for holding any reads that do not have a value for one or more of the
// attributes we're grouping by
private SAMFileGATKReadWriter createUnknownOutOnDemand(String attributeValue) {
    if (!attributeValue.equals("." + UNKNOWN_OUT_PREFIX)) {
        // attribute for which a given read/group has no value; anything else indicates a coding error
        throw new GATKException.ShouldNeverReachHereException("Unrecognized attribute value found: " + attributeValue);
    }
    final SAMFileWriterFactory samFileWriterFactory = new SAMFileWriterFactory();
    final SAMFileHeader samFileHeaderIn = getHeaderForReads();
    return prepareSAMFileWriter(samFileWriterFactory, samFileHeaderIn, attributeValue);
}

Example 3 with SAMFileWriterFactory

use of htsjdk.samtools.SAMFileWriterFactory in project gatk by broadinstitute.

the class CollectRnaSeqMetricsTest method testMultiLevel.

@Test
public void testMultiLevel() throws Exception {
    final String sequence = "chr1";
    final String ignoredSequence = "chrM";
    // Create some alignments that hit the ribosomal sequence, various parts of the gene, and intergenic.
    final SAMRecordSetBuilder builder = new SAMRecordSetBuilder(true, SAMFileHeader.SortOrder.coordinate, false);
    // Set seed so that strandedness is consistent among runs.
    builder.setRandomSeed(0);
    final int sequenceIndex = builder.getHeader().getSequenceIndex(sequence);
    final SAMReadGroupRecord rg1 = new SAMReadGroupRecord("2");
    rg1.setSample("Sample");
    rg1.setLibrary("foo");
    builder.setReadGroup(rg1);
    builder.addPair("pair1", sequenceIndex, 45, 475);
    builder.addPair("pair2", sequenceIndex, 90, 225);
    builder.addFrag("frag1", sequenceIndex, 150, true);
    builder.addFrag("frag2", sequenceIndex, 450, true);
    final SAMReadGroupRecord rg2 = new SAMReadGroupRecord("3");
    rg2.setSample("Sample");
    rg2.setLibrary("bar");
    builder.setReadGroup(rg2);
    builder.addPair("pair3", sequenceIndex, 120, 600);
    builder.addFrag("frag3", sequenceIndex, 225, false);
    builder.addPair("rrnaPair", sequenceIndex, 400, 500);
    builder.addFrag("ignoredFrag", builder.getHeader().getSequenceIndex(ignoredSequence), 1, false);
    final File samFile = BaseTest.createTempFile("tmp.collectRnaSeqMetrics.", ".sam");
    try (final SAMFileWriter samWriter = new SAMFileWriterFactory().makeSAMWriter(builder.getHeader(), false, samFile)) {
        for (final SAMRecord rec : builder.getRecords()) samWriter.addAlignment(rec);
    }
    // Create an interval list with one ribosomal interval.
    final Interval rRnaInterval = new Interval(sequence, 300, 520, true, "rRNA");
    final IntervalList rRnaIntervalList = new IntervalList(builder.getHeader());
    rRnaIntervalList.add(rRnaInterval);
    final File rRnaIntervalsFile = BaseTest.createTempFile("tmp.rRna.", ".interval_list");
    rRnaIntervalList.write(rRnaIntervalsFile);
    // Generate the metrics.
    final File metricsFile = BaseTest.createTempFile("tmp.", ".rna_metrics");
    final String[] args = new String[] { "--input", samFile.getAbsolutePath(), "--output", metricsFile.getAbsolutePath(), "--REF_FLAT", getRefFlatFile(sequence).getAbsolutePath(), "--RIBOSOMAL_INTERVALS", rRnaIntervalsFile.getAbsolutePath(), "--STRAND_SPECIFICITY", "SECOND_READ_TRANSCRIPTION_STRAND", "--IGNORE_SEQUENCE", ignoredSequence, "--LEVEL", "SAMPLE", "--LEVEL", "LIBRARY" };
    runCommandLine(args);
    final MetricsFile<RnaSeqMetrics, Comparable<?>> output = new MetricsFile<>();
    output.read(new FileReader(metricsFile));
    for (final RnaSeqMetrics metrics : output.getMetrics()) {
        if (metrics.LIBRARY == null) {
            Assert.assertEquals(metrics.PF_ALIGNED_BASES, 396);
            Assert.assertEquals(metrics.PF_BASES, 432);
            Assert.assertEquals(metrics.RIBOSOMAL_BASES.longValue(), 108L);
            Assert.assertEquals(metrics.CODING_BASES, 136);
            Assert.assertEquals(metrics.UTR_BASES, 51);
            Assert.assertEquals(metrics.INTRONIC_BASES, 50);
            Assert.assertEquals(metrics.INTERGENIC_BASES, 51);
            Assert.assertEquals(metrics.CORRECT_STRAND_READS, 3);
            Assert.assertEquals(metrics.INCORRECT_STRAND_READS, 4);
            Assert.assertEquals(metrics.IGNORED_READS, 1);
        } else if (metrics.LIBRARY.equals("foo")) {
            Assert.assertEquals(metrics.PF_ALIGNED_BASES, 216);
            Assert.assertEquals(metrics.PF_BASES, 216);
            Assert.assertEquals(metrics.RIBOSOMAL_BASES.longValue(), 36L);
            Assert.assertEquals(metrics.CODING_BASES, 89);
            Assert.assertEquals(metrics.UTR_BASES, 51);
            Assert.assertEquals(metrics.INTRONIC_BASES, 25);
            Assert.assertEquals(metrics.INTERGENIC_BASES, 15);
            Assert.assertEquals(metrics.CORRECT_STRAND_READS, 3);
            Assert.assertEquals(metrics.INCORRECT_STRAND_READS, 2);
            Assert.assertEquals(metrics.IGNORED_READS, 0);
        } else if (metrics.LIBRARY.equals("bar")) {
            Assert.assertEquals(metrics.PF_ALIGNED_BASES, 180);
            Assert.assertEquals(metrics.PF_BASES, 216);
            Assert.assertEquals(metrics.RIBOSOMAL_BASES.longValue(), 72L);
            Assert.assertEquals(metrics.CODING_BASES, 47);
            Assert.assertEquals(metrics.UTR_BASES, 0);
            Assert.assertEquals(metrics.INTRONIC_BASES, 25);
            Assert.assertEquals(metrics.INTERGENIC_BASES, 36);
            Assert.assertEquals(metrics.CORRECT_STRAND_READS, 0);
            Assert.assertEquals(metrics.INCORRECT_STRAND_READS, 2);
            Assert.assertEquals(metrics.IGNORED_READS, 1);
        }
    }
}

Example 4 with SAMFileWriterFactory

use of htsjdk.samtools.SAMFileWriterFactory in project hmftools by hartwigmedical.

the class Analysis method queryNameSortedBAM.

private static File queryNameSortedBAM(final SamReader reader, final QueryInterval[] intervals, final String name) throws IOException {
    final SAMFileHeader header = reader.getFileHeader().clone();
    header.setSortOrder(SAMFileHeader.SortOrder.queryname);
    final File file = File.createTempFile(name, ".bam");
    final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(header, false, file);
    final SAMRecordIterator iterator = reader.queryOverlapping(intervals);
    while (iterator.hasNext()) {
        writer.addAlignment(iterator.next());
    }
    iterator.close();
    writer.close();
    return file;
}

Example 5 with SAMFileWriterFactory

use of htsjdk.samtools.SAMFileWriterFactory in project hmftools by hartwigmedical.

the class BreakPointInspectorApplication method writeToSlice.

private static void writeToSlice(final String path, final SamReader reader, final QueryInterval[] intervals) {
    final File outputBAM = new File(path);
    final SAMFileWriter writer = new SAMFileWriterFactory().makeBAMWriter(reader.getFileHeader(), true, outputBAM);
    final SAMRecordIterator iterator = reader.queryOverlapping(intervals);
    while (iterator.hasNext()) {
        writer.addAlignment(iterator.next());
    }
    iterator.close();
    writer.close();
}