37 lines
1.0 KiB
Java
37 lines
1.0 KiB
Java
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package edu.mit.broad.picard.util;
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/**
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* A simple class that is used to store the coverage information about an interval.
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*
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* @author Tim Fennell
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*/
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public class Coverage {
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private Interval interval;
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private short[] depths;
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/** Constructs a new coverage object for the provided mapping with the desired padding either side. */
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public Coverage(Interval i, int padding) {
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this.interval = i;
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this.depths = new short[interval.length() + 2*padding];
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}
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/** Adds a single point of depth at the desired offset into the coverage array. */
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public void addBase(int offset) {
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if (offset >= 0 && offset < this.depths.length) {
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this.depths[offset] += 1;
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}
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}
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/** Returns true if any base in the range has coverage of > 1 */
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public boolean hasCoverage() {
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for (short s : depths) {
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if (s > 1) return true;
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}
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return false;
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}
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/** Gets the coverage depths as an array of shorts. */
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public short[] getDepths() { return this.depths; }
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}
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