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First draft of actual pooled EM caller. 

Produces sane looking output on region of 1kG pilot1:

   CALL NA12813.SRP000031.2009_02.bam CC 0.609084 0.609084
   CALL NA12003.SRP000031.2009_02.bam CC 2.114234 2.114234 CCCCC
   CALL NA06994.SRP000031.2009_02.bam CC 0.910114 0.910114 C
   CALL NA18940.SRP000031.2009_02.bam CT 2.589749 0.910114 T
   CALL NA18555.SRP000031.2009_02.bam CC 0.609084 0.609084

Next up, eval vs. Baseline pilot1 calls and pilot3 deep-coverage truth.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@526 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
jmaguire 2009-04-24 13:43:41 +00:00
parent dd408a2a9a
commit 4e4fd33584
1 changed files with 228 additions and 0 deletions
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java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCaller.java 100644
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package org.broadinstitute.sting.playground.gatk.walkers;
import net.sf.samtools.*;
import org.broadinstitute.sting.gatk.*;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
import org.broadinstitute.sting.gatk.refdata.rodGFF;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.LocusContext;
import org.broadinstitute.sting.playground.gatk.walkers.AlleleFrequencyWalker;
import org.broadinstitute.sting.playground.utils.AlleleFrequencyEstimate;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.cmdLine.Argument;
import java.util.*;
public class PoolCaller extends LocusWalker<AlleleFrequencyEstimate, String>
{
List<SingleSampleGenotyper> callers = null;
List<String> sample_names = null;
//@Argument(required=false, shortName="log_metrics", defaultValue="true") public boolean LOG_METRICS;
@Argument(required=false, shortName="fractional_counts", defaultValue="false") public boolean FRACTIONAL_COUNTS;
private Random random;
private SAMFileHeader header;
public void initialize()
{
GenomeAnalysisTK toolkit = this.getToolkit();
this.header = toolkit.getEngine().getSAMHeader();
List<SAMReadGroupRecord> read_groups = header.getReadGroups();
/*
GenomeAnalysisTK toolkit = this.getToolkit();
SAMFileHeader header = toolkit.getSamReader().getFileHeader();
List<SAMReadGroupRecord> read_groups = header.getReadGroups();
*/
sample_names = new ArrayList<String>();
callers = new ArrayList<SingleSampleGenotyper>();
random = new Random(42);
for (int i = 0; i < read_groups.size(); i++)
{
String sample_name = read_groups.get(i).getSample();
sample_names.add(sample_name);
//System.out.println("SAMPLE: " + sample_name);
SingleSampleGenotyper caller = new SingleSampleGenotyper();
caller.metricsFileName = "/dev/null";
caller.lodThreshold = 5.0;
caller.fourBaseMode = false;
caller.initialize();
callers.add(caller);
}
}
public AlleleFrequencyEstimate map(RefMetaDataTracker tracker, char ref, LocusContext context)
{
// 1. seperate each context.
LocusContext[] contexts = new LocusContext[sample_names.size()];
for (int i = 0; i < sample_names.size(); i++)
{
contexts[i] = filterLocusContext(context, sample_names.get(i), 0);
//System.out.printf("DEPTH %s %d\n", sample_names.get(i), contexts[i].getReads().size());
}
//System.out.printf("DEPTH %s %d\n", "TOTAL", context.getReads().size());
// EM Loop:
AlleleFrequencyEstimate[] calls = null;
double EM_alt_freq = 0;
double EM_N = 0;
// (this loop is the EM cycle)
EM_alt_freq = 0.5;
int num_iterations = 10;
double[] trajectory = new double[num_iterations + 1]; trajectory[0] = EM_alt_freq;
double[] likelihood_trajectory = new double[num_iterations + 1]; likelihood_trajectory[0] = 0.0;
for (int iterations = 0; iterations < num_iterations; iterations++)
{
// 6. Re-call from shallow coverage using the estimated frequency as a prior,
// and compare to true deep calls,
// and compute new MAF estimate.
calls = new AlleleFrequencyEstimate[sample_names.size()];
EM_N = 0.0;
double EM_sum = 0.0;
double likelihood = 0.0;
for (int i = 0; i < sample_names.size(); i++)
{
callers.get(i).setAlleleFrequencyPrior(EM_alt_freq);
calls[i] = callers.get(i).map(tracker, ref, contexts[i]);
String genotype = calls[i].genotype();
likelihood += calls[i].posterior();
//System.out.printf("DBG: %f %f %f %f\n",
// deep_calls[i].lodVsNextBest,
// deep_calls[i].lodVsRef,
// shallow_calls[i].lodVsNextBest,
// shallow_calls[i].lodVsRef);
if (! FRACTIONAL_COUNTS)
{
EM_sum += calls[i].emperical_allele_frequency() * calls[i].N;
EM_N += calls[i].N;
}
else
{
for (int j = 0; j <= calls[i].N; j++)
{
if (Double.isInfinite(calls[i].posteriors[j])) { calls[i].posteriors[j] = -10000; }
System.out.printf("DBG3: %d %f %d\n", j, calls[i].posteriors[j], calls[i].N);
EM_sum += Math.pow(10,calls[i].posteriors[j]) * (double)j;
EM_N += calls[i].N;
}
}
}
EM_alt_freq = EM_sum / EM_N;
trajectory[iterations+1] = EM_alt_freq;
likelihood_trajectory[iterations+1] = likelihood/(double)EM_N;
//System.out.printf("DBGTRAJ %f %f %f %f\n", EM_sum, EM_N, trajectory[iterations], trajectory[iterations+1]);
}
for (int i = 0; i < sample_names.size(); i++)
{
ReadBackedPileup pileup = new ReadBackedPileup(ref, contexts[i]);
System.out.printf("CALL %s %s %f %f %s\n", sample_names.get(i), calls[i].genotype(), calls[i].lodVsRef, calls[i].lodVsNextBest, pileup.getBases());
}
// 7. Compare to estimation from the pool.
System.out.printf("EVAL %s %f\n",
context.getLocation(),
EM_alt_freq);
//for (int i = 0; i < likelihood_trajectory.length; i++)
//{
// System.out.printf("TRAJECTORY %f %f\n", trajectory[i], likelihood_trajectory[i]);
//}
System.out.print("\n\n");
return null;
}
private LocusContext poolLocusContext(LocusContext[] contexts)
{
ArrayList<SAMRecord> reads = new ArrayList<SAMRecord>();
ArrayList<Integer> offsets = new ArrayList<Integer>();
GenomeLoc location = null;
for (int i = 0; i < contexts.length; i++)
{
if (contexts[i] != null)
{
location = contexts[i].getLocation();
reads.addAll(contexts[i].getReads());
offsets.addAll(contexts[i].getOffsets());
}
}
return new LocusContext(location, reads, offsets);
}
private LocusContext filterLocusContext(LocusContext context, String sample_name, int downsample)
{
ArrayList<SAMRecord> reads = new ArrayList<SAMRecord>();
ArrayList<Integer> offsets = new ArrayList<Integer>();
for (int i = 0; i < context.getReads().size(); i++)
{
SAMRecord read = context.getReads().get(i);
Integer offset = context.getOffsets().get(i);
String RG = (String)(read.getAttribute("RG"));
String sample = header.getReadGroup(RG).getSample();
if (sample == sample_name)
{
reads.add(read);
offsets.add(offset);
}
}
if (downsample != 0)
{
List<Integer> perm = new ArrayList<Integer>();
for (int i = 0; i < reads.size(); i++) { perm.add(i); }
perm = Utils.RandomSubset(perm, downsample);
ArrayList<SAMRecord> downsampled_reads = new ArrayList<SAMRecord>();
ArrayList<Integer> downsampled_offsets = new ArrayList<Integer>();
for (int i = 0; i < perm.size(); i++)
{
downsampled_reads.add(reads.get(perm.get(i)));
downsampled_offsets.add(offsets.get(perm.get(i)));
}
reads = downsampled_reads;
offsets = downsampled_offsets;
}
return new LocusContext(context.getLocation(), reads, offsets);
}
public void onTraversalDone()
{
return;
}
public String reduceInit()
{
return "";
}
public String reduce(AlleleFrequencyEstimate alleleFreq, String sum)
{
return "";
}
}