Useful walker that creates a new interval list with only the interval overlapping input sites list. Really a one-off walker
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/*
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* Copyright (c) 2010, 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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* 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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* 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 THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.oneoffprojects.walkers;
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import org.broadinstitute.sting.commandline.Argument;
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import org.broadinstitute.sting.commandline.Output;
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import org.broadinstitute.sting.commandline.Input;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
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import org.broadinstitute.sting.gatk.walkers.LocusWalker;
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import org.broadinstitute.sting.gatk.walkers.RefWalker;
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import org.broadinstitute.sting.gatk.walkers.RodWalker;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.GenomeLocParser;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import org.broadinstitute.sting.utils.text.XReadLines;
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import org.broadinstitute.sting.utils.collections.Pair;
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import org.broad.tribble.util.variantcontext.VariantContext;
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import java.util.List;
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import java.util.Collection;
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import java.util.ArrayList;
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import java.io.PrintStream;
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import java.io.InputStream;
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import java.io.File;
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import java.io.FileNotFoundException;
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import net.sf.picard.util.IntervalList;
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import net.sf.picard.util.Interval;
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/**
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* Counts the number of contiguous regions the walker traverses over. Slower than it needs to be, but
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* very useful since overlapping intervals get merged, so you can count the number of intervals the GATK merges down to.
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* This was its very first use.
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*/
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public class MarkIntervals extends RodWalker<Long, Long> {
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@Output
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File out;
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@Input(doc="List of bad SNP sites", required=true)
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File locs;
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List<GenomeLoc> badSites = new ArrayList<GenomeLoc>();
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IntervalList intervalList;
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@Argument(doc="Should we match intervals or just the sites?", required=false)
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boolean matchJustSites = false;
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public void initialize() {
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if ( this.getToolkit().getArguments().intervals.size() != 1 )
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throw new UserException("This walker only works with a single -L argument provided, sorry");
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File intervalFile = new File(this.getToolkit().getArguments().intervals.get(0));
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try {
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intervalList = IntervalList.fromFile(intervalFile);
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} catch ( Exception ex ) {
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throw new UserException.MalformedFile(intervalFile, "Couldn't read interval file", ex);
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}
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try {
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for ( String line : new XReadLines(locs, true) ) {
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String parts[] = line.split(":");
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badSites.add(GenomeLocParser.createGenomeLoc(parts[0], Long.valueOf(parts[1])));
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}
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} catch ( FileNotFoundException e ) {
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throw new UserException.CouldNotReadInputFile(locs, e);
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}
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}
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public Long reduceInit() {
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return 0l;
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}
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public boolean isReduceByInterval() { return true; }
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public Long map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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if ( tracker == null ) {
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return null;
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}
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return 0L;
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}
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public Long reduce(Long loc, Long prev) {
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return 0L;
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}
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public void onTraversalDone(List<Pair<GenomeLoc,Long>> finalReduce) {
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long nBadIntervals = 0;
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long nBadBases = 0;
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IntervalList badIntervals = new IntervalList(intervalList.getHeader());
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if ( matchJustSites ) {
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for ( GenomeLoc loc : badSites ) {
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nBadIntervals++;
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nBadBases += loc.size();
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badIntervals.add(new Interval(loc.getContig(), (int)loc.getStart(), (int)loc.getStop(), false, "nBadSites_" + 1));
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}
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} else {
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for ( Pair<GenomeLoc,Long> g : finalReduce ) {
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int overlaps = 0;
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GenomeLoc interval = g.getFirst();
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for ( GenomeLoc loc : badSites ) {
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if ( interval.overlapsP(loc) ) {
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logger.info(String.format("Overlapping %s with bad site %s", interval, loc));
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overlaps++;
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}
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}
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if ( overlaps > 0 ) {
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nBadIntervals++;
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nBadBases += interval.size();
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badIntervals.add(new Interval(interval.getContig(), (int)interval.getStart(), (int)interval.getStop(), false, "nBadSites_" + overlaps));
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//out.printf("%s %d%n", interval, overlaps);
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}
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}
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}
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logger.info("No. intervals marked as bad: " + nBadIntervals);
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logger.info("No. bases marked as bad: " + nBadBases);
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badIntervals.write(out);
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}
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}
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