Examples of SAMFileWriterFactory

Examples of htsjdk.samtools.SAMFileWriterFactory

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    protected int doWork() {
        IOUtil.assertFileIsReadable(INPUT);
        IOUtil.assertFileIsWritable(OUTPUT);
        final SAMFileReader reader = new SAMFileReader(INPUT);
        final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(reader.getFileHeader(), true, OUTPUT);

        if  (CREATE_INDEX && writer.getFileHeader().getSortOrder() != SAMFileHeader.SortOrder.coordinate){
            throw new PicardException("Can't CREATE_INDEX unless sort order is coordinate");
        }
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Examples of htsjdk.samtools.SAMFileWriterFactory

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        final boolean presorted = inputSortOrder.equals(outputHeader.getSortOrder());
        log.info("Filtering [presorted=" + presorted + "] " + INPUT.getName() + " -> OUTPUT=" +
            OUTPUT.getName() + " [sortorder=" + outputHeader.getSortOrder().name() + "]");

        // create OUTPUT file
        final SAMFileWriter outputWriter = new SAMFileWriterFactory().makeSAMOrBAMWriter(outputHeader, presorted, OUTPUT);

        final ProgressLogger progress = new ProgressLogger(log, (int) 1e6, "Written");
       
        while (filteringIterator.hasNext()) {
            final SAMRecord rec = filteringIterator.next();
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Examples of htsjdk.samtools.SAMFileWriterFactory

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    protected int doWork() {
        IOUtil.assertFileIsReadable(INPUT);
        IOUtil.assertFileIsWritable(OUTPUT);
        final SAMFileReader reader = new SAMFileReader(IOUtil.openFileForReading(INPUT));
        reader.getFileHeader().setSortOrder(SORT_ORDER);
        final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(reader.getFileHeader(), false, OUTPUT);
      writer.setProgressLogger(
          new ProgressLogger(log, (int) 1e7, "Wrote", "records from a sorting collection"));

        final ProgressLogger progress = new ProgressLogger(log, (int) 1e7, "Read");
        for (final SAMRecord rec: reader) {
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Examples of htsjdk.samtools.SAMFileWriterFactory

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        final SAMFileHeader header = headerMerger.getMergedHeader();
        for (final String comment : COMMENT) {
            header.addComment(comment);
        }
        header.setSortOrder(SORT_ORDER);
        final SAMFileWriterFactory samFileWriterFactory = new SAMFileWriterFactory();
        if (USE_THREADING) {
            samFileWriterFactory.setUseAsyncIo(true);
        }
        final SAMFileWriter out = samFileWriterFactory.makeSAMOrBAMWriter(header, presorted, OUTPUT);

        // Lastly loop through and write out the records
        final ProgressLogger progress = new ProgressLogger(log, PROGRESS_INTERVAL);
        while (iterator.hasNext()) {
            final SAMRecord record = iterator.next();
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Examples of htsjdk.samtools.SAMFileWriterFactory

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        final File alignedSam = File.createTempFile("aligned.", ".sam");
        alignedSam.deleteOnExit();
        final SAMFileHeader alignedHeader = new SAMFileHeader();
        alignedHeader.setSortOrder(SAMFileHeader.SortOrder.queryname);
        alignedHeader.setSequenceDictionary(new SAMFileReader(sequenceDict).getFileHeader().getSequenceDictionary());
        final SAMFileWriter alignedWriter = new SAMFileWriterFactory().makeSAMWriter(alignedHeader, true, alignedSam);
        for (int i = 0; i < Math.max(firstOfPair.size(), secondOfPair.size()); ++i) {
            final HitSpec firstHitSpec = firstOfPair.isEmpty()? null: firstOfPair.get(i);
            final HitSpec secondHitSpec = secondOfPair.isEmpty()? null: secondOfPair.get(i);
            final SAMRecord first = makeRead(alignedHeader, firstUnmappedRec, firstHitSpec, true, i);
            final SAMRecord second = makeRead(alignedHeader, secondUnmappedRec, secondHitSpec, false, i);
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Examples of htsjdk.samtools.SAMFileWriterFactory

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        final File alignedSam = File.createTempFile("aligned.", ".sam");
        alignedSam.deleteOnExit();
        final SAMFileHeader alignedHeader = new SAMFileHeader();
        alignedHeader.setSortOrder(SAMFileHeader.SortOrder.queryname);
        alignedHeader.setSequenceDictionary(new SAMFileReader(sequenceDict).getFileHeader().getSequenceDictionary());
        final SAMFileWriter alignedWriter = new SAMFileWriterFactory().makeSAMWriter(alignedHeader, true, alignedSam);
        for (int i = 0; i < hitSpecs.size(); ++i) {
            final HitSpec hitSpec = hitSpecs.get(i);
            final SAMRecord mappedRec = makeRead(alignedHeader, unmappedRec, hitSpec, i);
            if (mappedRec != null) {
                alignedWriter.addAlignment(mappedRec);
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Examples of htsjdk.samtools.SAMFileWriterFactory

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        final File output = File.createTempFile("mergeTest", ".sam");
        output.deleteOnExit();

        final File unmappedSam = File.createTempFile("unmapped.", ".sam");
        unmappedSam.deleteOnExit();
        final SAMFileWriterFactory factory = new SAMFileWriterFactory();
        final SAMFileHeader header = new SAMFileHeader();
        header.setSortOrder(SAMFileHeader.SortOrder.queryname);
        final String cigar = "16M";

        final SAMRecord firstOfPair = new SAMRecord(header);
        firstOfPair.setReadName("theRead");
        firstOfPair.setReadString("ACGTACGTACGTACGT");
        firstOfPair.setBaseQualityString("5555555555555555");
        firstOfPair.setReadUnmappedFlag(true);
        firstOfPair.setReadPairedFlag(true);
        firstOfPair.setFirstOfPairFlag(true);

        final SAMRecord secondOfPair = new SAMRecord(header);
        secondOfPair.setReadName("theRead");
        secondOfPair.setReadString("ACGTACGTACGTACGT");
        secondOfPair.setBaseQualityString("5555555555555555");
        secondOfPair.setReadUnmappedFlag(true);
        secondOfPair.setReadPairedFlag(true);
        secondOfPair.setSecondOfPairFlag(true);
        SamPairUtil.setMateInfo(firstOfPair, secondOfPair, header);

        final SAMFileWriter unmappedWriter = factory.makeSAMWriter(header, false, unmappedSam);
        unmappedWriter.addAlignment(firstOfPair);
        unmappedWriter.addAlignment(secondOfPair);
        unmappedWriter.close();

        final File alignedSam = File.createTempFile("aligned.", ".sam");
        alignedSam.deleteOnExit();

        // Populate the header with SAMSequenceRecords
        header.getSequenceDictionary().addSequence(new SAMSequenceRecord("chr1", 1000000));

        // Create 2 alignments for each end of pair
        final SAMFileWriter alignedWriter = factory.makeSAMWriter(header, false, alignedSam);
        for (int i = 1; i <= 2; ++i) {
            final SAMRecord firstOfPairAligned = new SAMRecord(header);
            firstOfPairAligned.setReadName(firstOfPair.getReadName());
            firstOfPairAligned.setReadBases(firstOfPair.getReadBases());
            firstOfPairAligned.setBaseQualities(firstOfPair.getBaseQualities());
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Examples of htsjdk.samtools.SAMFileWriterFactory

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     */
    private File[] createSamFilesToBeMerged(final MultipleAlignmentSpec[] specs) {
        try {
            final File unmappedSam = File.createTempFile("unmapped.", ".sam");
            unmappedSam.deleteOnExit();
            final SAMFileWriterFactory factory = new SAMFileWriterFactory();
            final SAMFileHeader header = new SAMFileHeader();
            header.setSortOrder(SAMFileHeader.SortOrder.queryname);
            final SAMRecord unmappedRecord = new SAMRecord(header);

            unmappedRecord.setReadName("theRead");
            unmappedRecord.setReadString("ACGTACGTACGTACGT");
            unmappedRecord.setBaseQualityString("5555555555555555");
            unmappedRecord.setReadUnmappedFlag(true);

            final SAMFileWriter unmappedWriter = factory.makeSAMWriter(header, false, unmappedSam);
            unmappedWriter.addAlignment(unmappedRecord);
            unmappedWriter.close();

            final File alignedSam = File.createTempFile("aligned.", ".sam");
            alignedSam.deleteOnExit();

            final String sequence = "chr1";
            // Populate the header with SAMSequenceRecords
            header.getSequenceDictionary().addSequence(new SAMSequenceRecord(sequence, 1000000));

            final SAMFileWriter alignedWriter = factory.makeSAMWriter(header, false, alignedSam);
            for (final MultipleAlignmentSpec spec : specs) {
                final SAMRecord alignedRecord = new SAMRecord(header);
                alignedRecord.setReadName(unmappedRecord.getReadName());
                alignedRecord.setReadBases(unmappedRecord.getReadBases());
                alignedRecord.setBaseQualities(unmappedRecord.getBaseQualities());
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Examples of htsjdk.samtools.SAMFileWriterFactory

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    private void testBestFragmentMapqStrategy(final String testName, final int[] firstMapQs, final int[] secondMapQs,
                                              final boolean includeSecondary, final int expectedFirstMapq,
                                              final int expectedSecondMapq) throws Exception {
        final File unmappedSam = File.createTempFile("unmapped.", ".sam");
        unmappedSam.deleteOnExit();
        final SAMFileWriterFactory factory = new SAMFileWriterFactory();
        final SAMFileHeader header = new SAMFileHeader();
        header.setSortOrder(SAMFileHeader.SortOrder.queryname);

        final String readName = "theRead";
        final SAMRecord firstUnmappedRead = new SAMRecord(header);
        firstUnmappedRead.setReadName(readName);
        firstUnmappedRead.setReadString("ACGTACGTACGTACGT");
        firstUnmappedRead.setBaseQualityString("5555555555555555");
        firstUnmappedRead.setReadUnmappedFlag(true);
        firstUnmappedRead.setMateUnmappedFlag(true);
        firstUnmappedRead.setReadPairedFlag(true);
        firstUnmappedRead.setFirstOfPairFlag(true);

        final SAMRecord secondUnmappedRead = new SAMRecord(header);
        secondUnmappedRead.setReadName(readName);
        secondUnmappedRead.setReadString("TCGAACGTTCGAACTG");
        secondUnmappedRead.setBaseQualityString("6666666666666666");
        secondUnmappedRead.setReadUnmappedFlag(true);
        secondUnmappedRead.setMateUnmappedFlag(true);
        secondUnmappedRead.setReadPairedFlag(true);
        secondUnmappedRead.setSecondOfPairFlag(true);



        final SAMFileWriter unmappedWriter = factory.makeSAMWriter(header, false, unmappedSam);
        unmappedWriter.addAlignment(firstUnmappedRead);
        unmappedWriter.addAlignment(secondUnmappedRead);
        unmappedWriter.close();

        final File alignedSam = File.createTempFile("aligned.", ".sam");
        alignedSam.deleteOnExit();

        final String sequence = "chr1";
        // Populate the header with SAMSequenceRecords
        header.getSequenceDictionary().addSequence(new SAMSequenceRecord(sequence, 1000000));

        final SAMFileWriter alignedWriter = factory.makeSAMWriter(header, false, alignedSam);

        addAlignmentsForBestFragmentMapqStrategy(alignedWriter, firstUnmappedRead, sequence, firstMapQs);
        addAlignmentsForBestFragmentMapqStrategy(alignedWriter, secondUnmappedRead, sequence, secondMapQs);
        alignedWriter.close();
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Examples of htsjdk.samtools.SAMFileWriterFactory

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        builder.addPair("rrnaPair", sequenceIndex, 400, 500);

        builder.addFrag("ignoredFrag", builder.getHeader().getSequenceIndex(ignoredSequence), 1, false);

        final File samFile = File.createTempFile("tmp.collectRnaSeqMetrics.", ".sam");
        final SAMFileWriter samWriter = new SAMFileWriterFactory().makeSAMWriter(builder.getHeader(), false, samFile);
        for (final SAMRecord rec: builder.getRecords()) samWriter.addAlignment(rec);
        samWriter.close();

        // Create an interval list with one ribosomal interval.
        final Interval rRnaInterval = new Interval(sequence, 300, 520, true, "rRNA");
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