Examples of htsjdk.samtools.GATKBin

htsjdk.samtools.GATKBin
A temporary solution to work around Java access rights issues: override GATKBin and make it public. TODO: Eliminate once we determine the final fate of the BAM index reading code.

            for (int ci = 0; ci < nChunks; ci++) {
                final long chunkBegin = rawChunkData[ci*2];
                final long chunkEnd = rawChunkData[ci*2+1];
                chunks.add(new GATKChunk(chunkBegin, chunkEnd));
            }
            GATKBin bin = new GATKBin(referenceSequence, indexBin);
            bin.setChunkList(chunks.toArray(new GATKChunk[chunks.size()]));
            while(indexBin >= bins.size())
                bins.add(null);
            bins.set(indexBin,bin);
        }

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     * Gets the level associated with the given bin number.
     * @param bin The bin  for which to determine the level.
     * @return the level associated with the given bin number.
     */
    public int getLevelForBin(final Bin bin) {
        GATKBin gatkBin = new GATKBin(bin);
        if(gatkBin.getBinNumber() >= MAX_BINS)
            throw new ReviewedGATKException("Tried to get level for invalid bin in index file " + mFile);
        for(int i = getNumIndexLevels()-1; i >= 0; i--) {
            if(gatkBin.getBinNumber() >= LEVEL_STARTS[i])
                return i;
        }
        throw new ReviewedGATKException("Unable to find correct bin for bin " + bin + " in index file " + mFile);
    }

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     */
    public int getFirstLocusInBin(final Bin bin) {
        final int level = getLevelForBin(bin);
        final int levelStart = LEVEL_STARTS[level];
        final int levelSize = ((level==getNumIndexLevels()-1) ? MAX_BINS-1 : LEVEL_STARTS[level+1]) - levelStart;
        return (new GATKBin(bin).getBinNumber() - levelStart)*(BIN_GENOMIC_SPAN /levelSize)+1;
    }

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     */
    public int getLastLocusInBin(final Bin bin) {
        final int level = getLevelForBin(bin);
        final int levelStart = LEVEL_STARTS[level];
        final int levelSize = ((level==getNumIndexLevels()-1) ? MAX_BINS-1 : LEVEL_STARTS[level+1]) - levelStart;
        return (new GATKBin(bin).getBinNumber()-levelStart+1)*(BIN_GENOMIC_SPAN /levelSize);
    }

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Related Classes of htsjdk.samtools.GATKBin

org.broadinstitute.gatk.engine.datasources.reads.GATKBAMIndex

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