117 lines
3.9 KiB
Java
117 lines
3.9 KiB
Java
/*
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* Copyright (c) 2012 The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package htsjdk.samtools;
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/**
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* A temporary solution to work around Java access rights issues:
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* override chunk and make it public.
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* TODO: Eliminate once we determine the final fate of the BAM index reading code.
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*/
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public class GATKChunk extends Chunk {
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/**
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* The average ratio of compressed block size / uncompressed block size, computed empirically
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* using the output of org.broadinstitute.gatk.engine.datasources.reads.utilities.PrintBGZFBounds.
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*/
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private static final double AVERAGE_BAM_COMPRESSION_RATIO = 0.39;
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public GATKChunk(final long start, final long stop) {
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super(start,stop);
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}
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public GATKChunk(final long blockStart, final int blockOffsetStart, final long blockEnd, final int blockOffsetEnd) {
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super(blockStart << 16 | blockOffsetStart,blockEnd << 16 | blockOffsetEnd);
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}
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public GATKChunk(final Chunk chunk) {
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super(chunk.getChunkStart(),chunk.getChunkEnd());
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}
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@Override
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public GATKChunk clone() {
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return new GATKChunk(getChunkStart(),getChunkEnd());
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}
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@Override
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public long getChunkStart() {
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return super.getChunkStart();
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}
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@Override
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public void setChunkStart(final long value) {
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super.setChunkStart(value);
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}
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@Override
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public long getChunkEnd() {
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return super.getChunkEnd();
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}
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@Override
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public void setChunkEnd(final long value) {
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super.setChunkEnd(value);
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}
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public long getBlockStart() {
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return getChunkStart() >>> 16;
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}
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public int getBlockOffsetStart() {
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return (int)(getChunkStart() & 0xFFFF);
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}
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public long getBlockEnd() {
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return getChunkEnd() >>> 16;
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}
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public int getBlockOffsetEnd() {
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return ((int)getChunkEnd() & 0xFFFF);
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}
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/**
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* Computes an approximation of the uncompressed size of the
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* chunk, in bytes. Can be used to determine relative weights
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* of chunk size.
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* @return An approximation of the chunk size in bytes.
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*/
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public long size() {
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final long chunkSpan = Math.round(((getChunkEnd()>>16)-(getChunkStart()>>16))/AVERAGE_BAM_COMPRESSION_RATIO);
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final int offsetSpan = (int)((getChunkEnd()&0xFFFF)-(getChunkStart()&0xFFFF));
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return chunkSpan + offsetSpan;
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}
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/**
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* Merges two chunks together. The caller is responsible for testing whether the
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* chunks overlap/are adjacent before calling this method!
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*
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* @param other the chunk to merge with this chunk
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* @return a new chunk representing the union of the two chunks (provided the chunks were
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* overlapping/adjacent)
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*/
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public GATKChunk merge ( GATKChunk other ) {
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return new GATKChunk(Math.min(getChunkStart(), other.getChunkStart()), Math.max(getChunkEnd(), other.getChunkEnd()));
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}
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}
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