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

Example 6 with SAMFileWriter

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

the class ReorderSam method doWork.

@Override
protected Object doWork() {
    IOUtil.assertFileIsReadable(INPUT);
    IOUtil.assertFileIsReadable(REFERENCE_SEQUENCE);
    IOUtil.assertFileIsWritable(OUTPUT);
    final SamReader in = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).open(INPUT);
    ReferenceSequenceFile reference = ReferenceSequenceFileFactory.getReferenceSequenceFile(REFERENCE_SEQUENCE);
    SAMSequenceDictionary refDict = reference.getSequenceDictionary();
    if (refDict == null) {
        CloserUtil.close(in);
        throw new UserException("No reference sequence dictionary found. Aborting. " + "You can create a sequence dictionary for the reference fasta using CreateSequenceDictionary.jar.");
    }
    printDictionary("SAM/BAM file", in.getFileHeader().getSequenceDictionary());
    printDictionary("Reference", refDict);
    Map<Integer, Integer> newOrder = buildSequenceDictionaryMap(refDict, in.getFileHeader().getSequenceDictionary());
    // has to be after we create the newOrder
    SAMFileHeader outHeader = ReadUtils.cloneSAMFileHeader(in.getFileHeader());
    outHeader.setSequenceDictionary(refDict);
    logger.info("Writing reads...");
    if (in.hasIndex()) {
        try (final SAMFileWriter out = createSAMWriter(OUTPUT, REFERENCE_SEQUENCE, outHeader, true)) {
            // write the reads in contig order
            for (final SAMSequenceRecord contig : refDict.getSequences()) {
                final SAMRecordIterator it = in.query(contig.getSequenceName(), 0, 0, false);
                writeReads(out, it, newOrder, contig.getSequenceName());
            }
            // don't forget the unmapped reads
            writeReads(out, in.queryUnmapped(), newOrder, "unmapped");
        }
    } else {
        try (final SAMFileWriter out = createSAMWriter(OUTPUT, REFERENCE_SEQUENCE, outHeader, false)) {
            writeReads(out, in.iterator(), newOrder, "All reads");
        }
    }
    // cleanup
    CloserUtil.close(in);
    return null;
}

Example 7 with SAMFileWriter

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

the class ReadUtilsUnitTest method testCreateSAMWriter.

@Test(dataProvider = "createSAMWriter")
public void testCreateSAMWriter(final File bamFile, final boolean preSorted, final boolean createIndex, final boolean createMD5, final boolean expectIndex) throws Exception {
    final File outputFile = createTempFile("samWriterTest", ".bam");
    try (final SamReader samReader = SamReaderFactory.makeDefault().open(bamFile)) {
        final SAMFileHeader header = samReader.getFileHeader();
        if (expectIndex) {
            // ensure test condition
            Assert.assertEquals(expectIndex, header.getSortOrder() == SAMFileHeader.SortOrder.coordinate);
        }
        try (final SAMFileWriter samWriter = ReadUtils.createCommonSAMWriter(outputFile, null, samReader.getFileHeader(), preSorted, createIndex, createMD5)) {
            final Iterator<SAMRecord> samRecIt = samReader.iterator();
            while (samRecIt.hasNext()) {
                samWriter.addAlignment(samRecIt.next());
            }
        }
    }
    final File md5File = new File(outputFile.getAbsolutePath() + ".md5");
    if (md5File.exists()) {
        md5File.deleteOnExit();
    }
    Assert.assertEquals(expectIndex, null != SamFiles.findIndex(outputFile));
    Assert.assertEquals(createMD5, md5File.exists());
}

Example 8 with SAMFileWriter

use of htsjdk.samtools.SAMFileWriter in project gatk-protected by broadinstitute.

the class AssemblyBasedCallerUtils method assembleReads.

/**
     * High-level function that runs the assembler on the given region's reads,
     * returning a data structure with the resulting information needed
     * for further HC steps
     */
public static AssemblyResultSet assembleReads(final AssemblyRegion region, final List<VariantContext> givenAlleles, final AssemblyBasedCallerArgumentCollection argumentCollection, final SAMFileHeader header, final SampleList sampleList, final Logger logger, final ReferenceSequenceFile referenceReader, final ReadThreadingAssembler assemblyEngine) {
    finalizeRegion(region, argumentCollection.errorCorrectReads, argumentCollection.dontUseSoftClippedBases, (byte) (argumentCollection.minBaseQualityScore - 1), header, sampleList);
    if (argumentCollection.debug) {
        logger.info("Assembling " + region.getSpan() + " with " + region.size() + " reads:    (with overlap region = " + region.getExtendedSpan() + ")");
    }
    final byte[] fullReferenceWithPadding = region.getAssemblyRegionReference(referenceReader, REFERENCE_PADDING_FOR_ASSEMBLY);
    final SimpleInterval paddedReferenceLoc = getPaddedReferenceLoc(region, REFERENCE_PADDING_FOR_ASSEMBLY, referenceReader);
    final Haplotype referenceHaplotype = createReferenceHaplotype(region, paddedReferenceLoc, referenceReader);
    final ReadErrorCorrector readErrorCorrector = argumentCollection.errorCorrectReads ? new ReadErrorCorrector(argumentCollection.assemblerArgs.kmerLengthForReadErrorCorrection, HaplotypeCallerEngine.MIN_TAIL_QUALITY_WITH_ERROR_CORRECTION, argumentCollection.assemblerArgs.minObservationsForKmerToBeSolid, argumentCollection.debug, fullReferenceWithPadding) : null;
    try {
        final AssemblyResultSet assemblyResultSet = assemblyEngine.runLocalAssembly(region, referenceHaplotype, fullReferenceWithPadding, paddedReferenceLoc, givenAlleles, readErrorCorrector, header);
        assemblyResultSet.debugDump(logger);
        return assemblyResultSet;
    } catch (final Exception e) {
        // Capture any exception that might be thrown, and write out the assembly failure BAM if requested
        if (argumentCollection.captureAssemblyFailureBAM) {
            try (final SAMFileWriter writer = ReadUtils.createCommonSAMWriter(new File("assemblyFailure.bam"), null, header, false, false, false)) {
                for (final GATKRead read : region.getReads()) {
                    writer.addAlignment(read.convertToSAMRecord(header));
                }
            }
        }
        throw e;
    }
}

Example 9 with SAMFileWriter

use of htsjdk.samtools.SAMFileWriter 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 10 with SAMFileWriter

use of htsjdk.samtools.SAMFileWriter 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();
}