Examples of AlignmentReader

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

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    private double madInsertSize;
    private static final int MAX_PAIRS = 10000;

    public static void main(String[] args) throws IOException {

        AlignmentReader reader = AlignmentReaderFactory.getReader(args[0], false);
        CloseableIterator<Alignment> iter = reader.iterator();
        PairedEndStats stats = compute(iter, .1, 99.9);
        iter.close();
        reader.close();

        System.out.println(args[0] + "\t" + stats.averageInsertSize + "\t" + stats.medianInsertSize +
                "\t" + stats.stddevInsertSize + "\t" + stats.madInsertSize);
    }
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Examples of org.broad.igv.sam.reader.AlignmentReader

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        this.minPercentileInsertSize = secondPercentileSize;
        this.maxPercentileInsertSize = maxPercentileInsertSize;
    }

    public static PairedEndStats compute(String bamFile) {
        AlignmentReader reader = null;
        try {
            reader = AlignmentReaderFactory.getReader(bamFile, false);
            final CloseableIterator<Alignment> alignmentCloseableIterator = reader.iterator();
            PairedEndStats stats = compute(alignmentCloseableIterator, .1, 99.9);
            alignmentCloseableIterator.close();
            return stats;

        } catch (IOException e) {
            log.error("Error reading sam file: " + e.getMessage(), e);
            return null;
        }
        finally {
            try {
                if (reader != null)
                    reader.close();
            } catch (IOException e) {
                log.error(e.getMessage(), e);
            }
        }
    }
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Examples of org.broad.igv.sam.reader.AlignmentReader

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    public static int writeAlignmentFilePicard(ResourceLocator inlocator, String outPath,
                                                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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