Examples of SamReader

        String chr = "chr1";
        int end = 300000000;
        int start = end / 5;


        BAMFileReader bamreader = new BAMFileReader(new File(bamfile));
        SAMReader samreader = new SAMReader(samfile);
        CloseableIterator<PicardAlignment> bamiter = bamreader.query(chr, start, end, true);
        CloseableIterator<PicardAlignment> samiter = samreader.iterator();
        int count = 0;
        while (bamiter.hasNext()) {
            Alignment bamrecord = bamiter.next();
            Alignment samrecord = samiter.next();
            assertTrue(bamrecord.getStart() >= start);

Examples of org.broad.igv.sam.reader.SAMReader

        private SAMFileHeader header;
        private List<PicardAlignment> alignments;


        public SamHeaderIterator(String inpath) throws IOException {


            SAMReader reader = new SAMReader(inpath, false);
            this.header = reader.getFileHeader();
            Iterator<PicardAlignment> iter = reader.iterator();


            alignments = new ArrayList<PicardAlignment>();
            while (iter.hasNext()) {
                alignments.add(iter.next());
            }

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