- Optimized implementation of -byReadGroup in DoCWalker
- Added implementation of -bySample in DoCWalker - Removed CoverageBySample and added a watered down version to the examples directory git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2209 348d0f76-0448-11de-a6fe-93d51630548a
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@ -0,0 +1,68 @@
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package org.broadinstitute.sting.gatk.examples;
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import net.sf.samtools.*;
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import org.broadinstitute.sting.gatk.refdata.*;
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import org.broadinstitute.sting.gatk.walkers.LocusWalker;
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import org.broadinstitute.sting.gatk.contexts.*;
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import org.broadinstitute.sting.utils.pileup.*;
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import java.util.*;
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public class CoverageBySample extends LocusWalker<Integer, Integer> {
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private HashSet<String> sampleNames = new HashSet<String>();
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public boolean requiresReads() { return true; }
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public void initialize() {
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List<SAMReadGroupRecord> read_groups = this.getToolkit().getSAMFileHeader().getReadGroups();
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for ( SAMReadGroupRecord record : read_groups ) {
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String sample = record.getSample();
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if ( sample != null )
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sampleNames.add(sample);
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}
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}
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public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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HashMap<String, Integer> depthBySample = new HashMap<String, Integer>();
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for ( String sample : sampleNames )
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depthBySample.put(sample, 0);
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ReadBackedPileup pileup = context.getPileup();
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for ( PileupElement p : pileup ) {
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SAMReadGroupRecord readGroup = p.getRead().getReadGroup();
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if ( readGroup == null )
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continue;
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String sample = readGroup.getSample();
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if ( sample != null ) {
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int oldDepth = depthBySample.get(sample);
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depthBySample.put(sample, oldDepth + 1);
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}
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}
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for ( Map.Entry<String, Integer> sample : depthBySample.entrySet() ) {
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out.printf(" %s %8d%n", sample.getKey(), sample.getValue());
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}
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return 1;
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}
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public void onTraversalDone(Integer result) {
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out.println("Processed " + result + " loci.");
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}
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public Integer reduceInit() {
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return 0;
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}
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public Integer reduce(Integer value, Integer sum) {
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return sum + value;
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}
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}
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@ -32,9 +32,7 @@ import org.broadinstitute.sting.utils.Pair;
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import org.broadinstitute.sting.utils.pileup.*;
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import net.sf.samtools.SAMReadGroupRecord;
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import java.util.HashMap;
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import java.util.Collections;
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import java.util.ArrayList;
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import java.util.*;
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/**
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* Display the depth of coverage at a given locus.
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@ -48,16 +46,25 @@ public class DepthOfCoverageWalker extends LocusWalker<Integer, Pair<Long, Long>
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}
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@Argument(fullName="printStyle", shortName = "s", doc="Printing style: NONE, COMPACT, or DETAILED", required=false)
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public printType printStyle = printType.COMPACT;
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protected printType printStyle = printType.COMPACT;
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@Argument(fullName="excludeDeletions", shortName = "ed", doc="If true, we will exclude reads with deletions at a locus in coverage",required=false)
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public boolean excludeDeletionsInCoverage = false;
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protected boolean excludeDeletionsInCoverage = false;
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@Argument(fullName="minMAPQ", shortName = "minMAPQ", doc="If provided, we will exclude reads with MAPQ < this value at a locus in coverage",required=false)
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public int excludeMAPQBelowThis = -1;
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protected int excludeMAPQBelowThis = -1;
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@Argument(fullName="byReadGroup", shortName="byRG", doc="List read depths for each read group")
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public boolean byReadGroup = false;
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protected boolean byReadGroup = false;
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@Argument(fullName="bySample", shortName="bySample", doc="List read depths for each sample")
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protected boolean bySample = false;
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private TreeSet<String> readGroupNames = new TreeSet<String>();
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private TreeSet<String> sampleNames = new TreeSet<String>();
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public boolean includeReadsWithDeletionAtLoci() { return ! excludeDeletionsInCoverage; }
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@ -70,15 +77,32 @@ public class DepthOfCoverageWalker extends LocusWalker<Integer, Pair<Long, Long>
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out.printf("locus nCleanReads nDeletionReads nLowMAPQReads%n");
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break;
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}
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if ( byReadGroup ) {
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List<SAMReadGroupRecord> readGroups = this.getToolkit().getSAMFileHeader().getReadGroups();
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for ( SAMReadGroupRecord record : readGroups )
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readGroupNames.add(record.getReadGroupId());
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}
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if ( bySample ) {
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List<SAMReadGroupRecord> readGroups = this.getToolkit().getSAMFileHeader().getReadGroups();
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for ( SAMReadGroupRecord record : readGroups ) {
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String sample = record.getSample();
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if ( sample != null )
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sampleNames.add(sample);
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}
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}
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}
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public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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int nCleanReads = 0, nBadMAPQReads = 0, nDeletionReads = 0;
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HashMap<String, Integer> depthByReadGroup = new HashMap<String, Integer>();
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for (SAMReadGroupRecord rg : this.getToolkit().getSAMFileHeader().getReadGroups()) {
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depthByReadGroup.put(rg.getReadGroupId(), 0);
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}
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for ( String readGroupName : readGroupNames )
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depthByReadGroup.put(readGroupName, 0);
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HashMap<String, Integer> depthBySample = new HashMap<String, Integer>();
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for ( String sample : sampleNames )
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depthBySample.put(sample, 0);
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ReadBackedPileup pileup = context.getPileup();
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for ( PileupElement p : pileup ) {
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@ -87,9 +111,23 @@ public class DepthOfCoverageWalker extends LocusWalker<Integer, Pair<Long, Long>
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else if ( p.isDeletion() ) nDeletionReads++;
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else nCleanReads++;
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String readGroupName = p.getRead().getReadGroup().getReadGroupId();
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int oldDepth = depthByReadGroup.get(readGroupName);
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depthByReadGroup.put(readGroupName, oldDepth + 1);
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SAMReadGroupRecord readGroup = p.getRead().getReadGroup();
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if ( readGroup == null )
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continue;
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if ( byReadGroup ) {
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String readGroupName = readGroup.getReadGroupId();
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int oldDepth = depthByReadGroup.get(readGroupName);
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depthByReadGroup.put(readGroupName, oldDepth + 1);
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}
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if ( bySample ) {
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String sample = readGroup.getSample();
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if ( sample != null ) {
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int oldDepth = depthBySample.get(sample);
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depthBySample.put(sample, oldDepth + 1);
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}
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}
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}
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int nTotalReads = nCleanReads + (excludeDeletionsInCoverage ? 0 : nDeletionReads);
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@ -103,15 +141,18 @@ public class DepthOfCoverageWalker extends LocusWalker<Integer, Pair<Long, Long>
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break;
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}
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if (byReadGroup) {
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ArrayList<String> rgs = new ArrayList<String>(depthByReadGroup.keySet());
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Collections.sort(rgs);
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for (String rg : rgs) {
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if ( byReadGroup ) {
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for ( String rg : readGroupNames ) {
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out.printf(" %s %8d%n", rg, depthByReadGroup.get(rg));
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}
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}
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if ( bySample ) {
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for ( String sample : sampleNames ) {
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out.printf(" %s %8d%n", sample, depthBySample.get(sample));
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}
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}
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return nTotalReads;
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}
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@ -1,185 +0,0 @@
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package org.broadinstitute.sting.playground.gatk.walkers;
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import net.sf.samtools.*;
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import org.broadinstitute.sting.gatk.*;
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import org.broadinstitute.sting.gatk.refdata.*;
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import org.broadinstitute.sting.gatk.walkers.LocusWalker;
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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.utils.Utils;
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import org.broadinstitute.sting.utils.BaseUtils;
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import java.util.*;
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public class CoverageBySample extends LocusWalker<String, String>
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{
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List<String> sample_names = null;
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public boolean requiresReads() { return true; }
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private SAMFileHeader header;
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public void initialize()
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{
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GenomeAnalysisEngine toolkit = this.getToolkit();
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this.header = toolkit.getSAMFileHeader();
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List<SAMReadGroupRecord> read_groups = header.getReadGroups();
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sample_names = new ArrayList<String>();
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HashSet<String> unique_sample_names = new HashSet<String>();
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for (int i = 0; i < read_groups.size(); i++)
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{
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String sample_name = read_groups.get(i).getSample();
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if (unique_sample_names.contains(sample_name)) { continue; }
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unique_sample_names.add(sample_name);
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sample_names.add(sample_name);
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}
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}
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public String map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context)
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{
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String line = context.getLocation().getContig() + " " + context.getLocation().getStart() + " " ;
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AlignmentContext[] contexts = filterAlignmentContext(context, sample_names, 0);
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HashMap<String,Integer> counts = countReadsBySample(context);
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for (int i = 0; i < contexts.length; i++)
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{
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List<SAMRecord> reads = contexts[i].getReads();
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List<Integer> offsets = contexts[i].getOffsets();
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out.printf("%s %s ", context.getLocation(), sample_names.get(i));
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int[] forward_counts = new int[4];
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int[] backward_counts = new int[4];
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for (int j = 0; j < reads.size(); j++)
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{
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SAMRecord read = reads.get(j);
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int offset = offsets.get(j);
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boolean backward = read.getReadNegativeStrandFlag();
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char base = Character.toUpperCase((char)(read.getReadBases()[offset]));
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if (BaseUtils.simpleBaseToBaseIndex(base) == -1) { continue; }
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if (backward) { base = Character.toLowerCase(base); }
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if (! backward) { forward_counts[BaseUtils.simpleBaseToBaseIndex(base)]++; }
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else { backward_counts[BaseUtils.simpleBaseToBaseIndex(base)]++; }
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//out.printf("%c", base);
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}
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out.printf("A[%d] C[%d] G[%d] T[%d] a[%d] c[%d] g[%d] t[%d]",
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forward_counts[0],
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forward_counts[1],
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forward_counts[2],
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forward_counts[3],
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backward_counts[0],
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backward_counts[1],
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backward_counts[2],
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backward_counts[3]);
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out.printf("\n");
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}
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return "";
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}
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private HashMap<String,Integer> countReadsBySample(AlignmentContext context)
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{
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HashMap<String,Integer> counts = new HashMap<String,Integer>();
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for (int i = 0; i < sample_names.size(); i++)
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{
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counts.put(sample_names.get(i), 0);
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}
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for (int i = 0; i < context.getReads().size(); i++)
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{
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SAMRecord read = context.getReads().get(i);
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String sample = read.getReadGroup().getSample();
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counts.put(sample, counts.get(sample)+1);
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}
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return counts;
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}
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private AlignmentContext[] filterAlignmentContext(AlignmentContext context, List<String> sample_names, int downsample)
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{
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HashMap<String,Integer> index = new HashMap<String,Integer>();
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for (int i = 0; i < sample_names.size(); i++)
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{
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index.put(sample_names.get(i), i);
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}
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AlignmentContext[] contexts = new AlignmentContext[sample_names.size()];
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ArrayList<SAMRecord>[] reads = new ArrayList[sample_names.size()];
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ArrayList<Integer>[] offsets = new ArrayList[sample_names.size()];
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for (int i = 0; i < sample_names.size(); i++)
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{
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reads[i] = new ArrayList<SAMRecord>();
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offsets[i] = new ArrayList<Integer>();
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}
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for (int i = 0; i < context.getReads().size(); i++)
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{
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SAMRecord read = context.getReads().get(i);
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Integer offset = context.getOffsets().get(i);
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assert(header != null);
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assert(read.getReadGroup() != null);
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String sample = read.getReadGroup().getSample();
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//if (SAMPLE_NAME_REGEX != null) { sample = sample.replaceAll(SAMPLE_NAME_REGEX, "$1"); }
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reads[index.get(sample)].add(read);
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offsets[index.get(sample)].add(offset);
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}
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if (downsample != 0)
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{
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for (int j = 0; j < reads.length; j++)
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{
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List<Integer> perm = new ArrayList<Integer>();
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for (int i = 0; i < reads[j].size(); i++) { perm.add(i); }
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perm = Utils.RandomSubset(perm, downsample);
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ArrayList<SAMRecord> downsampled_reads = new ArrayList<SAMRecord>();
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ArrayList<Integer> downsampled_offsets = new ArrayList<Integer>();
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for (int i = 0; i < perm.size(); i++)
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{
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downsampled_reads.add(reads[j].get(perm.get(i)));
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downsampled_offsets.add(offsets[j].get(perm.get(i)));
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}
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reads[j] = downsampled_reads;
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offsets[j] = downsampled_offsets;
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contexts[j] = new AlignmentContext(context.getLocation(), reads[j], offsets[j]);
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}
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}
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else
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{
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for (int j = 0; j < reads.length; j++)
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{
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contexts[j] = new AlignmentContext(context.getLocation(), reads[j], offsets[j]);
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}
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}
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return contexts;
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}
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public void onTraversalDone(String result)
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{
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return;
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}
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public String reduceInit()
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{
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return "";
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}
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public String reduce(String line, String sum)
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{
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return "";
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}
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}
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