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

Example 11 with SAMFileWriterFactory

use of htsjdk.samtools.SAMFileWriterFactory in project ASCIIGenome by dariober.

the class Utils method sortAndIndexSamOrBam.

/**
 * Sort and index input sam or bam.
 * @throws IOException
 */
public static void sortAndIndexSamOrBam(String inSamOrBam, String sortedBam, boolean deleteOnExit) throws IOException {
    /*  ------------------------------------------------------ */
    /* This chunk prepares SamReader from local bam or URL bam */
    UrlValidator urlValidator = new UrlValidator();
    SamReaderFactory srf = SamReaderFactory.make();
    srf.validationStringency(ValidationStringency.SILENT);
    SamReader samReader;
    if (urlValidator.isValid(inSamOrBam)) {
        samReader = SamReaderFactory.makeDefault().open(SamInputResource.of(new URL(inSamOrBam)));
    } else {
        samReader = srf.open(new File(inSamOrBam));
    }
    /*  ------------------------------------------------------ */
    samReader.getFileHeader().setSortOrder(SortOrder.coordinate);
    File out = new File(sortedBam);
    if (deleteOnExit) {
        out.deleteOnExit();
        File idx = new File(out.getAbsolutePath().replaceAll("\\.bam$", "") + ".bai");
        idx.deleteOnExit();
    }
    SAMFileWriter outputSam = new SAMFileWriterFactory().setCreateIndex(true).makeSAMOrBAMWriter(samReader.getFileHeader(), false, out);
    for (final SAMRecord samRecord : samReader) {
        outputSam.addAlignment(samRecord);
    }
    samReader.close();
    outputSam.close();
}

Example 12 with SAMFileWriterFactory

use of htsjdk.samtools.SAMFileWriterFactory in project gridss by PapenfussLab.

the class StubFastqAligner method align.

@Override
public void align(File fastq, File output, File reference, int threads) throws IOException {
    SAMFileHeader header = context.getBasicSamHeader();
    try (FastqReader reader = new FastqReader(fastq)) {
        try (SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(header, true, output)) {
            for (FastqRecord fqr : reader) {
                SAMRecord source = nameLookup.get(fqr.getReadName());
                SAMRecord r = new SAMRecord(header);
                r.setReadName(fqr.getReadName());
                r.setReadBases(fqr.getReadString().getBytes());
                r.setBaseQualities(SAMUtils.fastqToPhred(fqr.getBaseQualityString()));
                if (source == null) {
                    r.setReadUnmappedFlag(true);
                } else {
                    ChimericAlignment aln = map.get(fqr.getReadName());
                    r.setReferenceName(aln.rname);
                    r.setAlignmentStart(aln.pos);
                    r.setCigar(aln.cigar);
                    r.setMappingQuality(aln.mapq);
                    r.setAttribute("NM", aln.nm);
                    if (aln.isNegativeStrand) {
                        SequenceUtil.reverseComplement(r.getReadBases());
                        ArrayUtils.reverse(r.getBaseQualities());
                    }
                }
                writer.addAlignment(r);
            }
        }
    }
}

Example 13 with SAMFileWriterFactory

use of htsjdk.samtools.SAMFileWriterFactory in project gridss by PapenfussLab.

the class SmithWatermanFastqAligner method align.

@Override
public void align(File fastq, File output, File reference, int threads) throws IOException {
    try (ReferenceSequenceFile ref = new IndexedFastaSequenceFile(reference)) {
        SAMFileHeader header = new SAMFileHeader();
        header.setSequenceDictionary(ref.getSequenceDictionary());
        byte[] bases = ref.getSequence(ref.getSequenceDictionary().getSequence(referenceIndex).getSequenceName()).getBases();
        try (FastqReader reader = new FastqReader(fastq)) {
            try (SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(header, true, output)) {
                for (FastqRecord fqr : reader) {
                    Alignment aln = aligner.align_smith_waterman(fqr.getReadString().getBytes(), bases);
                    SAMRecord r = new SAMRecord(header);
                    r.setReadName(fqr.getReadName());
                    r.setReferenceIndex(referenceIndex);
                    r.setAlignmentStart(aln.getStartPosition() + 1);
                    r.setCigarString(aln.getCigar());
                    r.setReadBases(fqr.getReadString().getBytes());
                    r.setBaseQualities(SAMUtils.fastqToPhred(fqr.getBaseQualityString()));
                    writer.addAlignment(r);
                }
            }
        }
    }
}

Example 14 with SAMFileWriterFactory

use of htsjdk.samtools.SAMFileWriterFactory in project gridss by PapenfussLab.

the class ComputeSamTags method doWork.

@Override
protected int doWork() {
    log.debug("Setting language-neutral locale");
    java.util.Locale.setDefault(Locale.ROOT);
    validateParameters();
    SamReaderFactory readerFactory = SamReaderFactory.make();
    SAMFileWriterFactory writerFactory = new SAMFileWriterFactory();
    try {
        try (SamReader reader = readerFactory.open(INPUT)) {
            SAMFileHeader header = reader.getFileHeader();
            if (!ASSUME_SORTED) {
                if (header.getSortOrder() != SortOrder.queryname) {
                    log.error("INPUT is not sorted by queryname. " + "ComputeSamTags requires that reads with the same name be sorted together. " + "If the input file satisfies this constraint (the output from many aligners do)," + " this check can be disabled with the ASSUME_SORTED option.");
                    return -1;
                }
            }
            try (SAMRecordIterator it = reader.iterator()) {
                File tmpoutput = gridss.Defaults.OUTPUT_TO_TEMP_FILE ? FileSystemContext.getWorkingFileFor(OUTPUT, "gridss.tmp.ComputeSamTags.") : OUTPUT;
                try (SAMFileWriter writer = writerFactory.makeSAMOrBAMWriter(header, true, tmpoutput)) {
                    compute(it, writer, getReference(), TAGS, SOFTEN_HARD_CLIPS, FIX_MATE_INFORMATION, RECALCULATE_SA_SUPPLEMENTARY, INPUT.getName() + "-");
                }
                if (tmpoutput != OUTPUT) {
                    FileHelper.move(tmpoutput, OUTPUT, true);
                }
            }
        }
    } catch (IOException e) {
        log.error(e);
        return -1;
    }
    return 0;
}

Example 15 with SAMFileWriterFactory

use of htsjdk.samtools.SAMFileWriterFactory in project gridss by PapenfussLab.

the class ExtractSVReads method setup.

@Override
protected void setup(SAMFileHeader header, File samFile) {
    if (METRICS_OUTPUT != null) {
        metricsCollector = new CollectStructuralVariantReadMetrics();
        copyInput(metricsCollector);
        metricsCollector.OUTPUT = METRICS_OUTPUT;
        metricsCollector.setup(header, samFile);
    }
    SAMFileWriterFactory writerFactory = new SAMFileWriterFactory();
    if (header.getSortOrder() != SortOrder.queryname) {
        log.info("Not considering multiple read alignments as the input file is not queryname sorted.");
    }
    tmpoutput = gridss.Defaults.OUTPUT_TO_TEMP_FILE ? FileSystemContext.getWorkingFileFor(OUTPUT, "gridss.tmp.ExtractSVReads.") : OUTPUT;
    writer = writerFactory.makeSAMOrBAMWriter(header, true, tmpoutput);
    IndelReadFilter indelFilter = new IndelReadFilter(INDELS ? MIN_INDEL_SIZE : Integer.MAX_VALUE);
    ClippedReadFilter softClipFilter = new ClippedReadFilter(CLIPPED ? MIN_CLIP_LENGTH : Integer.MAX_VALUE);
    SplitReadFilter splitReadFilter = new SplitReadFilter();
    AlignedFilter unmappedFilter = new AlignedFilter(false);
    OneEndAnchoredReadFilter oeaFilter = new OneEndAnchoredReadFilter();
    ReadPairConcordanceFilter dpFilter = getReadPairConcordanceCalculator() != null ? new ReadPairConcordanceFilter(getReadPairConcordanceCalculator(), false, true) : null;
    List<SamRecordFilter> readfilters = new ArrayList<>();
    readfilters.add(indelFilter);
    readfilters.add(softClipFilter);
    if (SPLIT)
        readfilters.add(splitReadFilter);
    if (UNMAPPED_READS)
        readfilters.add(unmappedFilter);
    readfilter = new UnionAggregateFilter(readfilters);
    List<SamRecordFilter> pairfilters = new ArrayList<>();
    if (SINGLE_MAPPED_PAIRED)
        pairfilters.add(oeaFilter);
    if (dpFilter != null && DISCORDANT_READ_PAIRS)
        pairfilters.add(dpFilter);
    pairfilter = new UnionAggregateFilter(pairfilters);
    if (!SINGLE_MAPPED_PAIRED && !DISCORDANT_READ_PAIRS) {
        pairfilter = new FixedFilter(true);
    }
    count = 0;
}