Package htsjdk.samtools

Examples of htsjdk.samtools.SAMFileWriterFactory

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    public int execute() {
        long readsWritten = 0;
        long readsAltered = 0;

        SAMFileReader reader = new SAMFileReader(input);
        SAMFileWriter writer = new SAMFileWriterFactory().makeBAMWriter(reader.getFileHeader(),true,output,compressionLevel);

        for(SAMRecord read: reader) {
            Object value = read.getAttribute(sourceTagName);
            if(value != null) {
                read.setAttribute(sourceTagName,null);
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            tempFile = File.createTempFile("testfile_"+getMaxReads(),".bam");
        }
        catch(IOException ex) {
            throw new ReviewedGATKException("Unable to create temporary BAM",ex);
        }
        SAMFileWriterFactory factory = new SAMFileWriterFactory();
        factory.setCreateIndex(true);
        SAMFileWriter writer = factory.makeBAMWriter(fullInputFile.getFileHeader(),true,tempFile);

        long numReads = 0;
        for(SAMRecord read: fullInputFile) {
            if(numReads++ >= getMaxReads())
                break;
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        if (VALIDATION_STRINGENCY == ValidationStringency.STRICT) {
            SAMFileReader.setDefaultValidationStringency(ValidationStringency.LENIENT);
        }
        try {
            final SAMFileReader reader = new SAMFileReader(INPUT);
            final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(reader.getFileHeader(), true, OUTPUT);
            final CloseableIterator<SAMRecord> it = reader.iterator();
            final ProgressLogger progress = new ProgressLogger(Log.getInstance(CleanSam.class));

            // If the read (or its mate) maps off the end of the alignment, clip it
            while(it.hasNext()) {
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        IOUtil.assertFileIsReadable(INPUT);
        IOUtil.assertFileIsWritable(OUTPUT);

        final Random r = RANDOM_SEED == null ? new Random() : new Random(RANDOM_SEED);
        final SAMFileReader in = new SAMFileReader(INPUT);
        final SAMFileWriter out = new SAMFileWriterFactory().makeSAMOrBAMWriter(in.getFileHeader(), true, OUTPUT);
        final Map<String,Boolean> decisions = new HashMap<String,Boolean>();

        long total = 0;
        long kept  = 0;
       
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        if (!REMOVE_ALIGNMENT_INFORMATION) {
            outHeader.setSequenceDictionary(inHeader.getSequenceDictionary());
            outHeader.setProgramRecords(inHeader.getProgramRecords());
        }

        final SAMFileWriter out = new SAMFileWriterFactory().makeSAMOrBAMWriter(outHeader, presorted, OUTPUT);

        ////////////////////////////////////////////////////////////////////////////
        // Build a sorting collection to use if we are sanitizing
        ////////////////////////////////////////////////////////////////////////////
        final SortingCollection<SAMRecord> sorter;
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        final SAMFileReader recordReader = new SAMFileReader(INPUT);
        if (replacementHeader.getSortOrder() != recordReader.getFileHeader().getSortOrder()) {
            throw new PicardException("Sort orders of INPUT (" + recordReader.getFileHeader().getSortOrder().name() +
            ") and HEADER (" + replacementHeader.getSortOrder().name() + ") do not agree.");
        }
        final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(replacementHeader, true, OUTPUT);

        final ProgressLogger progress = new ProgressLogger(Log.getInstance(ReplaceSamHeader.class));
        for (final SAMRecord rec : recordReader) {
            rec.setHeader(replacementHeader);
            writer.addAlignment(rec);
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        IOUtil.assertFileIsReadable(FASTQ);
        IOUtil.assertFileIsWritable(OUTPUT);
       
        final FastqReader freader = new FastqReader(FASTQ,ALLOW_AND_IGNORE_EMPTY_LINES);
        final SAMFileHeader header = createFileHeader();
        final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(header, false, OUTPUT);

        int readCount = 0;
        final ProgressLogger progress = new ProgressLogger(LOG);
        for ( ; freader.hasNext()  ; readCount++) {
            final FastqRecord frec = freader.next();
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        IOUtil.assertFileIsWritable(OUTPUT);
       
        final FastqReader freader1 = new FastqReader(FASTQ,ALLOW_AND_IGNORE_EMPTY_LINES);
        final FastqReader freader2 = new FastqReader(FASTQ2,ALLOW_AND_IGNORE_EMPTY_LINES);
        final SAMFileHeader header = createFileHeader() ;
        final SAMFileWriter writer = (new SAMFileWriterFactory()).makeSAMOrBAMWriter(header, false, OUTPUT);

        int readCount = 0;
        final ProgressLogger progress = new ProgressLogger(LOG);
        for ( ; freader1.hasNext() && freader2.hasNext() ; readCount++) {
            final FastqRecord frec1 = freader1.next();
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        final SAMFileHeader outHeader = inHeader.clone();
        if (null == SORT_ORDER) this.SORT_ORDER = inHeader.getSortOrder(); // same as the input
        outHeader.setSortOrder(SORT_ORDER);
        SAMFileWriterFactory.setDefaultCreateIndexWhileWriting(CREATE_INDEX);
        SAMFileWriterFactory.setDefaultCreateMd5File(CREATE_MD5_FILE);
        final SAMFileWriter out = new SAMFileWriterFactory().makeSAMOrBAMWriter(outHeader, false, OUTPUT);

        // Iterate over the records, revert original base qualities, and push them into a SortingCollection by queryname
        final SortingCollection<SAMRecord> sorter = SortingCollection.newInstance(SAMRecord.class, new BAMRecordCodec(outHeader),
                new SAMRecordQueryNameComparator(), MAX_RECORDS_IN_RAM);
        final ProgressLogger revertingProgress = new ProgressLogger(log, 1000000, " reverted OQs");
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        final SAMFileReader in = new SAMFileReader(INPUT);
        final SAMFileHeader.SortOrder order = in.getFileHeader().getSortOrder();
        SAMFileWriter out = null;
        if (OUTPUT != null) {
            IOUtil.assertFileIsWritable(OUTPUT);
            out = new SAMFileWriterFactory().makeSAMOrBAMWriter(in.getFileHeader(), true, OUTPUT);
        }

        final Histogram<Integer> histo = new Histogram<Integer>("clipped_bases", "read_count");

        // Combine any adapters and custom adapter pairs from the command line into an array for use in clipping
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Related Classes of htsjdk.samtools.SAMFileWriterFactory

  • org.broadinstitute.gatk.engine.datasources.reads.ReadProcessingBenchmark
  • org.broadinstitute.gatk.engine.datasources.reads.utilities.BAMTagRenamer
  • picard.analysis.CollectRnaSeqMetricsTest
  • picard.illumina.IlluminaBasecallsToSam
  • picard.illumina.MarkIlluminaAdapters
  • picard.sam.AbstractAlignmentMerger
  • picard.sam.AddOrReplaceReadGroups
  • picard.sam.CleanSam
  • picard.sam.CreateSequenceDictionary
  • picard.sam.DownsampleSam
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