Examples of org.broad.igv.sam.reader.AlignmentReader.query()

Class org.broad.igv.sam.reader.AlignmentReader

Examples of org.broad.igv.sam.reader.AlignmentReader.query()

org.broad.igv.sam.reader.AlignmentReader.query()
Query alignments over a given range. Be careful about start/end, SAMTools uses 1-based, but IGV uses 0-based. This function requires hasIndex() == true. @param sequence @param start 0-based start location @param end 0-based, exclusive-end coordinate @param contained @return @throws IOException




    private AlignmentInterval getAlignmentInterval() throws Exception {
        ResourceLocator rl = new ResourceLocator(path);
        AlignmentReader samReader = AlignmentReaderFactory.getReader(rl);
        CloseableIterator<Alignment> iter = samReader.query(chr, start, end, contained);
        List<Alignment> list = new ArrayList<Alignment>();
        while(iter.hasNext()){
            list.add(iter.next());
        }
        AlignmentInterval interval = new AlignmentInterval(chr, start, end, list, null, null, null);

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     */
    public void tstQuery(String testFile, String sequence, int start, int end, boolean contained, int maxDepth) throws IOException {


        ResourceLocator loc = new ResourceLocator(testFile);
        AlignmentReader reader = AlignmentReaderFactory.getReader(loc);
        CloseableIterator<Alignment> iter = reader.query(sequence, start, end, contained);


        List<Alignment> expectedResult = new ArrayList<Alignment>();
        while (iter.hasNext()) {
            Alignment rec = iter.next();

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            if (queryInterval == null) {
                reader = AlignmentReaderFactory.getReader(alignmentFile, false);
                iter = reader.iterator();
            } else {
                reader = AlignmentReaderFactory.getReader(alignmentFile, true);
                iter = reader.query(queryInterval.getChr(), queryInterval.getStart() - 1, queryInterval.getEnd(), false);
            }


            while (iter != null && iter.hasNext()) {
                Alignment alignment = iter.next();
                if (passFilter(alignment)) {

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                                                String sequence, int start, int end) throws IOException{


        checkExportableAlignmentFile(inlocator.getTypeString());


        AlignmentReader reader = AlignmentReaderFactory.getReader(inlocator);
        CloseableIterator<PicardAlignment> iter = reader.query(sequence, start, end, false);
        final SAMFileHeader fileHeader = reader.getFileHeader();


        SAMWriter writer = new SAMWriter(fileHeader);
        int count = writer.writeToFile(new File(outPath), iter, true);
        iter.close();

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