Examples of BAMRecordCodec

htsjdk.samtools.BAMRecordCodec

Examples of htsjdk.samtools.BAMRecordCodec

            return mergingIterator;
        }




        final SortingCollection<SAMRecord> alignmentSorter = SortingCollection.newInstance(SAMRecord.class,
                    new BAMRecordCodec(header), new SAMRecordQueryNameComparator(), MAX_RECORDS_IN_RAM);


        int count = 0;
        while (mergingIterator.hasNext()) {
            alignmentSorter.add(mergingIterator.next());
            count++;

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Examples of htsjdk.samtools.BAMRecordCodec

            this.numRecords = numRecords;
            this.bamCodec = bamCodec;
        }


        Codec(final int numRecords) {
            this(numRecords, new BAMRecordCodec(null));
        }

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Examples of htsjdk.samtools.BAMRecordCodec

        ////////////////////////////////////////////////////////////////////////////
        // Build a sorting collection to use if we are sanitizing
        ////////////////////////////////////////////////////////////////////////////
        final SortingCollection<SAMRecord> sorter;
        if (sanitizing) {
            sorter = SortingCollection.newInstance(SAMRecord.class, new BAMRecordCodec(outHeader), new SAMRecordQueryNameComparator(), MAX_RECORDS_IN_RAM);
        }
        else {
            sorter = null;
        }

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Examples of htsjdk.samtools.BAMRecordCodec

        HitsForInsert nextAligned = nextAligned();


        // Create the sorting collection that will write the records in the coordinate order
        // to the final bam file
        final SortingCollection<SAMRecord> sorted = SortingCollection.newInstance(
            SAMRecord.class, new BAMRecordCodec(header), new SAMRecordCoordinateComparator(),
            MAX_RECORDS_IN_RAM);


        while (unmappedIterator.hasNext()) {
            // Load next unaligned read or read pair.
            final SAMRecord rec = unmappedIterator.next();

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Examples of htsjdk.samtools.BAMRecordCodec

                iterator = new SamPairUtil.SetMateInfoIterator(new PeekableIterator<SAMRecord>(tmp), ADD_MATE_CIGAR);
            }
            else {
                log.info("Sorting input into queryname order.");
                final SortingCollection<SAMRecord> sorter = SortingCollection.newInstance(SAMRecord.class,
                                                                                          new BAMRecordCodec(header),
                                                                                          new SAMRecordQueryNameComparator(),
                                                                                          MAX_RECORDS_IN_RAM,
                                                                                          TMP_DIR);
                while (tmp.hasNext()) {
                    sorter.add(tmp.next());

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Examples of htsjdk.samtools.BAMRecordCodec

        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");
        int numOriginalQualitiesRestored = 0;
        for (final SAMRecord record : in) {
            // Clean up reads that map off the end of the reference

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