Got Kris's permission to delete these walkers.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2200 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks
parent
3180fffd43
commit
e581cceab6
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@ -1,123 +0,0 @@
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package org.broadinstitute.sting.playground.gatk.walkers;
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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.walkers.LocusWalker;
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import org.broadinstitute.sting.utils.cmdLine.Argument;
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import net.sf.samtools.SAMRecord;
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import java.util.List;
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public class Pilot3CoverageWalker extends LocusWalker<Integer, Integer> {
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@Argument(fullName = "extended", shortName="ext", doc="extended output", required=false)
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public boolean extendedOutput = false;
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@Argument(fullName="min_mapq", shortName="mmq", required=false, doc="Minimum mapping quality of reads to consider") public Integer MIN_MAPQ = 1;
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public void initialize() {
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out.println("track type=wiggle_0 name=Pilot3Coverage viewLimits=0:1");
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}
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public String walkerType() { return "ByLocus"; }
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// Do we actually want to operate on the context?
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public boolean filter(RefMetaDataTracker tracker, char ref, AlignmentContext context) {
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return true; // We are keeping all the reads
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}
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// Map over the org.broadinstitute.sting.gatk.contexts.AlignmentContext
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int MAPPING_QUALITY_THRESHOLD = 1;
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int totalSites;
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int tumorCovered;
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int normalCovered;
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int somaticCovered;
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long start = 0;
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int lastContigIndex = -1;
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long lastPosition = -1;
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public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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if (start ==0) { start = System.currentTimeMillis(); }
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List<SAMRecord> reads = context.getReads();
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int totalDepth = 0;
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int positiveStrandDepth = 0;
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int negativeStrandDepth = 0;
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for ( int i = 0; i < reads.size(); i++ )
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{
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SAMRecord read = reads.get(i);
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// TODO: could this be done better elsewhere?
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// only process primary, non duplicate alignments
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// that come from fully mapped pairs with a mappign quality threshold >= x
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if (read.getNotPrimaryAlignmentFlag() ||
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read.getDuplicateReadFlag() ||
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read.getReadUnmappedFlag() ||
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read.getMappingQuality() < MIN_MAPQ
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// ||
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// read.getMateUnmappedFlag() ||
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) {
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continue;
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}
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totalDepth++;
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if (read.getReadNegativeStrandFlag()) {
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negativeStrandDepth++;
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} else {
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positiveStrandDepth++;
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}
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}
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// if the contig index has changed OR if it's the same contig index but we jumped positions
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// output a wiggle header
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StringBuilder sb = new StringBuilder();
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if (lastContigIndex != context.getLocation().getContigIndex() ||
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lastPosition + 1 != context.getPosition()) {
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lastContigIndex = context.getLocation().getContigIndex();
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sb.append("fixedStep").append(" ")
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.append("chrom=").append(context.getContig()).append(" ")
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.append("start=").append(context.getPosition()).append(" ")
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.append("step=1")
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.append("\n");
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}
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lastPosition = context.getPosition();
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if (extendedOutput) {
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sb.append(context.getPosition()).append(" ");
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sb.append(totalDepth).append(" ");
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sb.append(positiveStrandDepth).append(" ");
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sb.append(negativeStrandDepth).append(" ");
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}
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boolean siteCovered = (totalDepth >= 10 && positiveStrandDepth >= 2 && negativeStrandDepth >= 2);
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sb.append((siteCovered)?"1":"0");
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out.println(sb.toString());
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return 1;
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}
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// Given result of map function
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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 value + sum;
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}
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@Override
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public void onTraversalDone(Integer result) {
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// out.println(String.format("FINAL - %d %d %d %d", totalSites, tumorCovered, normalCovered, somaticCovered));
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}
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}
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@ -1,423 +0,0 @@
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package org.broadinstitute.sting.playground.gatk.walkers;
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import edu.mit.broad.picard.genotype.DiploidGenotype;
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import net.sf.picard.PicardException;
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import net.sf.samtools.SAMRecord;
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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.HapMapAlleleFrequenciesROD;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
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import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
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import org.broadinstitute.sting.gatk.walkers.LocusWalker;
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import org.broadinstitute.sting.utils.Utils;
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import org.broadinstitute.sting.utils.cmdLine.Argument;
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import static java.lang.Math.log10;
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import java.util.Arrays;
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import java.util.Formatter;
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import java.util.List;
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public class PopPriorWalker extends LocusWalker<Integer, Integer> {
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@Argument(fullName = "quality_score_cutoff", doc="quality score cutoff", required = false) public Byte qualityScoreCutoff;
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public PopPriorWalker() {
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}
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public void initialize() {
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}
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public String walkerType() { return "ByLocus"; }
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// Do we actually want to operate on the context?
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public boolean filter(RefMetaDataTracker tracker, char ref, AlignmentContext context) {
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return true; // We are keeping all the reads
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}
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protected class OldAndBustedGenotypeLikelihoods
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{
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public double[] likelihoods;
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public String[] genotypes;
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OldAndBustedGenotypeLikelihoods()
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{
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likelihoods = new double[10];
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genotypes = new String[10];
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genotypes[0] = "AA";
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genotypes[1] = "AC";
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genotypes[2] = "AG";
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genotypes[3] = "AT";
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genotypes[4] = "CC";
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genotypes[5] = "CG";
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genotypes[6] = "CT";
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genotypes[7] = "GG";
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genotypes[8] = "GT";
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genotypes[9] = "TT";
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}
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void add(char ref, char read, byte qual)
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{
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double p_error = Math.pow(10.0, (double)qual / -10);
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for (int i = 0; i < genotypes.length; i++)
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{
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likelihoods[i] += AlleleLikelihood(ref, read, genotypes[i], p_error);
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}
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}
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double AlleleLikelihood(char ref, char read, String genotype, double p_error)
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{
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char h1 = genotype.charAt(0);
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char h2 = genotype.charAt(1);
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double p_base;
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if ((h1 == h2) && (h1 == read)) { p_base = Math.log10(1-p_error); }
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else if ((h1 != h2) && (h1 == read) || (h2 == read)) { p_base = Math.log10(0.5 - (p_error/2.0)); }
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else { p_base = Math.log10(p_error); }
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return p_base;
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}
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// TODO: horrible horrible idea... but it's ok for right now. should really
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// implement this more cleanly so you can get sorted genotypes without losing the
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// ability to call add
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public void doSort() {
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Integer[] permutation = Utils.SortPermutation(likelihoods);
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String[] sorted_genotypes = Utils.PermuteArray(genotypes, permutation);
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double[] sorted_likelihoods = Utils.PermuteArray(likelihoods, permutation);
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this.genotypes = sorted_genotypes;
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this.likelihoods = sorted_likelihoods;
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}
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}
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// Map over the org.broadinstitute.sting.gatk.contexts.AlignmentContext
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public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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char upRef = Character.toUpperCase(ref.getBase());
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List<SAMRecord> reads = context.getReads();
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List<Integer> offsets = context.getOffsets();
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// Look up hapmap and dbsnp priors
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String rodString = "";
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rodDbSNP dbsnpInfo = null;
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HapMapAlleleFrequenciesROD hapmap = null;
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for ( ReferenceOrderedDatum datum : tracker.getAllRods() )
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{
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if ( datum != null )
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{
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if ( datum instanceof rodDbSNP) {
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dbsnpInfo = (rodDbSNP)datum;
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} else if (datum instanceof HapMapAlleleFrequenciesROD) {
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hapmap = (HapMapAlleleFrequenciesROD) datum;
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}
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}
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}
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// Accumulate genotype likelihoods
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int aCount = 0;
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int cCount = 0;
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int gCount = 0;
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int tCount = 0;
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OldAndBustedGenotypeLikelihoods glAll = new OldAndBustedGenotypeLikelihoods();
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OldAndBustedGenotypeLikelihoods glForward = new OldAndBustedGenotypeLikelihoods();
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OldAndBustedGenotypeLikelihoods glReverse = new OldAndBustedGenotypeLikelihoods();
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for ( int i = 0; i < reads.size(); i++ )
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{
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SAMRecord read = reads.get(i);
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// TODO: could this be done better elsewhere?
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if (read.getNotPrimaryAlignmentFlag() || read.getDuplicateReadFlag() || read.getReadUnmappedFlag()) {
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continue;
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}
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int offset = offsets.get(i);
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char base = (char)read.getReadBases()[offset];
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byte qual = read.getBaseQualities()[offset];
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if (qual == 0) { continue; }
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if (qualityScoreCutoff != null && qual < qualityScoreCutoff) { continue; }
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if (base == 'A') { aCount++; }
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if (base == 'C') { cCount++; }
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if (base == 'G') { gCount++; }
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if (base == 'T') { tCount++; }
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// System.out.println(read.getReadName() + " " + base + " " + qual );
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glAll.add(ref.getBase(), base, qual);
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if (read.getReadNegativeStrandFlag()) {
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glReverse.add(ref.getBase(), base, qual);
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} else {
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glForward.add(ref.getBase(), base, qual);
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}
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}
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// apply priors
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String priorType = "NONE";
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double[] priors;
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// hapmap overrides dbsnp which overrides "novel"
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if (hapmap != null) {
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List<String> knownAlleles = hapmap.getAllelesFWD();
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priorType = "HAPMAP";
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rodString = "[HAPMAP" + hapmap.toSimpleString() + "]";
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priors = getKnownSiteKnownFreqPriors(((byte)(upRef & 0xff)), knownAlleles, hapmap.getVarAlleleFreq());
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} else if (dbsnpInfo != null && dbsnpInfo.isSNP()) {
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List<String> knownAlleles = Arrays.asList(Utils.join("",dbsnpInfo.getAlleleList()));
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priorType = "DBSNP";
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rodString = "[DBSNP: " + dbsnpInfo.toMediumString() + "]";
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priors = getKnownSitePriors(((byte)(upRef & 0xff)), knownAlleles);
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} else {
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priors = getNovelSitePriors(((byte)(upRef & 0xff)));
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}
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StringBuilder priorString = new StringBuilder();
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priorString.append(priorType);
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for(int i=0; i<priors.length; i++) {
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// apply the prior!!!
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double log10prior = log10(priors[i]);
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glAll.likelihoods[i] += log10prior;
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glForward.likelihoods[i] += log10prior;
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glReverse.likelihoods[i] += log10prior;
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priorString.append(" ");
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priorString
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.append(glAll.genotypes[i])
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.append(":")
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.append(new Formatter().format("%4.2f",log10prior));
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}
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// FIXME: horrible way to do this!!!!
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glAll.doSort();
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glForward.doSort();
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glReverse.doSort();
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String gt = glAll.genotypes[glAll.genotypes.length-1];
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double btnb = glAll.likelihoods[glAll.genotypes.length-1] - glAll.likelihoods[glAll.genotypes.length-2];
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double btr = 1.0d; // FIXME: do we need this?
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// just to mimic old behavior
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String type = "homozygous";
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if (gt.charAt(0) != gt.charAt(1)) { type = "heterozygous-SNP"; }
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else if (gt.charAt(0) != upRef) { type = "homozygous-SNP"; }
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out.print(String.format("%s %d %s %s %4.6f %4.6f %s A:%d C:%d G:%d T:%d %d ",
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context.getContig(),
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context.getPosition(),
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upRef,
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gt,
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btnb,
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btr,
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type,
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aCount,
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cCount,
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gCount,
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tCount,
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aCount + cCount + gCount + tCount));
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out.print(dumpTheories(glAll));
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out.print(String.format("%s %s ",
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priorString,
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rodString));
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out.print(dumpTheories(glForward));
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out.print(dumpTheories(glReverse));
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out.print("\n");
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return 1;
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}
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// Given result of map function
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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 value + sum;
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}
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@Override
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public void onTraversalDone(Integer result) {
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}
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protected static final double NOVEL_HET_PRIOR = 2*1E-4;
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protected static final double NOVEL_OTHER_PRIOR = 1E-5;
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protected static final double NOVEL_REF_PRIOR = 1d - 4*NOVEL_HET_PRIOR - 6*NOVEL_OTHER_PRIOR;
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protected static final double KNOWN_HET_PRIOR = .05;
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protected static final double KNOWN_HNREF_PRIOR = .05*.05;
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protected static final double KNOWN_OTHER_PRIOR = 1E-5;
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protected static final double KNOWN_REF_PRIOR = 1d - KNOWN_HET_PRIOR - KNOWN_HNREF_PRIOR - 8* KNOWN_OTHER_PRIOR;
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protected static final double FREQ_OTHER_PRIOR = 1E-5;
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public double[] getNovelSitePriors(final byte referenceBase) {
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//TODO: convert everything to use DiploidGenotype
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DiploidGenotype[] theories = DiploidGenotype.values();
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double[] priors = new double[theories.length];
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DiploidGenotype refTheory = DiploidGenotype.fromBases(referenceBase, referenceBase);
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// use novel variant prior
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// ref (e.g. AA) -> 1 - 4*(2*10^-4) - 6*(10^-5)
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// het (e.g. AC, AG, AT) -> 2*10^-4 (AC, AG, AT,
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// other (e.g. CC, CG, CT, GG, GT, TT) -> 10^-5
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int i=0;
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for (DiploidGenotype theory : theories) {
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double prior = 0;
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if (theory == refTheory) {
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prior = NOVEL_REF_PRIOR;
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} else if (theory.getAllele1() == referenceBase || theory.getAllele2() == referenceBase) {
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prior = NOVEL_HET_PRIOR;
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} else { // not reference, and not het with reference base
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prior = NOVEL_OTHER_PRIOR;
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}
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priors[i++] = prior;
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}
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return priors;
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}
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public double[] getKnownSitePriors(final byte referenceBase,
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final List<String> alleles) {
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//TODO: convert everything to use DiploidGenotype
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DiploidGenotype[] theories = DiploidGenotype.values();
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double[] priors = new double[theories.length];
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DiploidGenotype refTheory = DiploidGenotype.fromBases(referenceBase, referenceBase);
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if (alleles != null && alleles.size() > 2 ) {
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// FIXME: handle multi-allele case!
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return getNovelSitePriors(referenceBase);
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}
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StringBuilder sb = new StringBuilder();
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if (alleles != null ) {
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for(String allele : alleles) { sb.append(allele); }
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}
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String allelesString = sb.toString();
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DiploidGenotype knownAlleles = DiploidGenotype.fromBases(allelesString.getBytes());
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byte altAllele = getAlternateAllele(knownAlleles, referenceBase);
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DiploidGenotype hnref = DiploidGenotype.fromBases(altAllele, altAllele);
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// do we not have a freq (in dbsnp, known alleles)
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// AA -
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// AG - .05
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// GG - .05^2
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// other - 10^-5
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int i=0;
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for (DiploidGenotype theory : theories) {
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double prior = 0;
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if (theory == refTheory) {
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prior = KNOWN_REF_PRIOR;
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} else if (theory == knownAlleles) {
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prior = KNOWN_HET_PRIOR;
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} else if (theory == hnref) {
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prior = KNOWN_HNREF_PRIOR;
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} else {
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prior = NOVEL_OTHER_PRIOR;
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}
|
||||
priors[i++] = prior;
|
||||
}
|
||||
|
||||
return priors;
|
||||
|
||||
}
|
||||
|
||||
public double[] getKnownSiteKnownFreqPriors(final byte referenceBase,
|
||||
final List<String> alleles,
|
||||
final Double altAllelefrequency) {
|
||||
|
||||
//TODO: convert everything to use DiploidGenotype
|
||||
DiploidGenotype[] theories = DiploidGenotype.values();
|
||||
double[] priors = new double[theories.length];
|
||||
|
||||
DiploidGenotype refTheory = DiploidGenotype.fromBases(referenceBase, referenceBase);
|
||||
|
||||
// if we're dealing with more than one allele here... make sure they all have no frequency data
|
||||
if (alleles != null && alleles.size() > 2 ) {
|
||||
throw new PicardException("Can't handle multiple known alleles with a single known frequency!");
|
||||
}
|
||||
|
||||
|
||||
StringBuilder sb = new StringBuilder();
|
||||
if (alleles != null ) {
|
||||
for(String allele : alleles) { sb.append(allele); }
|
||||
}
|
||||
String allelesString = sb.toString();
|
||||
|
||||
|
||||
// System.out.println("FREQ");
|
||||
// assert that we have just one set of frequencies...
|
||||
//FIXME: if (aaf.size() > 1) { throw new PicardException("Attempting to call with multiple allele frequencies!"); }
|
||||
DiploidGenotype knownAlleles = DiploidGenotype.fromBases(allelesString.getBytes());
|
||||
byte altAllele = getAlternateAllele(knownAlleles, referenceBase);
|
||||
DiploidGenotype hnref = DiploidGenotype.fromBases(altAllele, altAllele);
|
||||
|
||||
double q = altAllelefrequency;
|
||||
double p = 1d - q;
|
||||
|
||||
|
||||
// do we have a freq (in hapmap, known alleles)
|
||||
// AA -
|
||||
// AG -
|
||||
// GG -
|
||||
// other - 10^-5
|
||||
int i=0;
|
||||
for (DiploidGenotype theory : theories) {
|
||||
double prior = 0;
|
||||
if (theory == refTheory) {
|
||||
prior = p*p; //TODO: should this really sum to 1?
|
||||
} else if (theory == knownAlleles) {
|
||||
prior = 2*p*q;
|
||||
} else if (theory == hnref) {
|
||||
prior = q*q;
|
||||
} else {
|
||||
prior = FREQ_OTHER_PRIOR;
|
||||
}
|
||||
priors[i++] = prior;
|
||||
}
|
||||
|
||||
|
||||
return priors;
|
||||
}
|
||||
|
||||
protected byte getAlternateAllele(final DiploidGenotype gt, final byte refAllele) {
|
||||
return (gt.getAllele1() == refAllele)?gt.getAllele2():gt.getAllele1();
|
||||
}
|
||||
|
||||
protected String dumpTheories(OldAndBustedGenotypeLikelihoods gl) {
|
||||
StringBuilder sb = new StringBuilder();
|
||||
for (int i = gl.genotypes.length-1; i >= 0; i--)
|
||||
{
|
||||
sb.append(String.format("%s:%4.2f ", gl.genotypes[i], gl.likelihoods[i]));
|
||||
}
|
||||
return sb.toString();
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
Loading…
Reference in New Issue