84 lines
2.7 KiB
Java
84 lines
2.7 KiB
Java
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package edu.mit.broad.arachne;
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import java.io.BufferedReader;
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import java.io.File;
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import java.io.FileReader;
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import java.io.IOException;
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import java.util.BitSet;
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import java.util.SortedMap;
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import java.util.TreeMap;
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/**
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* Utility class to read in a set of contig-based genomic intervals in zero-based end inclusive
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* and store them efficiently in memory as a 1-based bit-mask
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*/
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public class GenomeMask {
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// if memory usage becomes a problem... this could be changed to a SparseBitSet
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// http://java.sun.com/developer/onlineTraining/collections/magercises/BitSet/index.html
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private SortedMap<Integer, BitSet> data = new TreeMap<Integer, BitSet>();
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public GenomeMask(File maskFile) throws IOException {
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BufferedReader baitReader = null;
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try {
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baitReader = new BufferedReader(new FileReader(maskFile));
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String line;
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while ((line = baitReader.readLine()) != null) {
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String[] arr = line.split(" ");
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int contig = Integer.parseInt(arr[0]);
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// covert the coordinates from 0-based, end inclusive to
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// 1-based end inclusive
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int startPos = Integer.parseInt(arr[1]) + 1;
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int endPos = Integer.parseInt(arr[2]) + 1;
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BitSet bits = data.get(contig);
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if (bits == null) {
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bits = new BitSet(endPos);
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data.put(contig,bits);
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}
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bits.set(startPos, endPos + 1); // set method is end exclusive
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}
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} finally {
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if (baitReader != null) { baitReader.close(); }
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}
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}
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/**
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* This ctor is useful if initializing a GenomeMask externally.
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*/
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public GenomeMask() {
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}
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public boolean get(int contig, int position) {
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BitSet bits = data.get(contig);
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return (bits != null) && bits.get(position);
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}
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public BitSet get(int contig) {
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return data.get(contig);
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}
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/**
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* Get an existing BitSet for the given contig, or create one if not already present. This is
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* useful when initializing a GenomeMask from an external source.
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* @param contig which BitSet
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* @param numBits if there was not already a BitSet for this contig, one is created and initialized to this size.
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* @return the BitSet for the given contig, creating one if necessary
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*/
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public BitSet getOrCreate(int contig, int numBits) {
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BitSet ret = data.get(contig);
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if (ret == null) {
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ret = new BitSet(numBits);
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data.put(contig, ret);
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}
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return ret;
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}
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public int getMaxContig() {
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return data.lastKey();
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}
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}
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