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Strand test and misc touch-ups 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@871 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
jmaguire 2009-06-01 17:13:21 +00:00
parent fc91e3e30e
commit 417f5b145e
3 changed files with 145 additions and 36 deletions
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124
java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCaller.java
View File

@ -101,8 +101,35 @@ public class PoolCaller extends LocusWalker<AlleleFrequencyEstimate, String>
public AlleleFrequencyEstimate map(RefMetaDataTracker tracker, char ref, LocusContext context)
{
if (ref == 'N') { return null; }
ref = Character.toUpperCase(ref);
// 1. seperate each context.
// seperate each context.
LocusContext forward = filterLocusContextByStrand(context, "+");
LocusContext backward = filterLocusContextByStrand(context, "-");
if (forward.getReads().size() == 0) { return null; }
if (backward.getReads().size() == 0) { return null; }
AlleleFrequencyEstimate estimate_both = EM(tracker, ref, context);
AlleleFrequencyEstimate estimate_forward = EM(tracker, ref, forward);
AlleleFrequencyEstimate estimate_backward = EM(tracker, ref, backward);
discovery_output_file.printf("%s %c %f %c %f\n",
estimate_both.asPoolTabularString(),
estimate_forward.alt,
estimate_forward.lodVsRef,
estimate_backward.alt,
estimate_backward.lodVsRef);
//discovery_output_file.printf("%s\n", estimate_forward.asPoolTabularString());
//discovery_output_file.printf("%s\n", estimate_backward.asPoolTabularString());
//discovery_output_file.printf("\n");
return null;
}
private AlleleFrequencyEstimate EM(RefMetaDataTracker tracker, char ref, LocusContext context)
{
if (context.getReads().size() == 0) { return null; }
LocusContext[] contexts = filterLocusContext(context, sample_names, 0);
// EM Loop:
@ -160,6 +187,8 @@ public class PoolCaller extends LocusWalker<AlleleFrequencyEstimate, String>
calls[i] = callers.get(i).map(tracker, ref, contexts[i]);
String genotype = calls[i].genotype();
if (calls[i].depth == 0) { continue; }
likelihood += calls[i].pBest;
if (! FRACTIONAL_COUNTS)
@ -200,33 +229,61 @@ public class PoolCaller extends LocusWalker<AlleleFrequencyEstimate, String>
}
// 7. Output some statistics.
double discovery_posterior = 0;
double discovery_likelihood = 0;
double discovery_null = 0;
double discovery_prior = 0;
double discovery_null_prior = 0;
int n_ref = 0;
int n_het = 0;
int n_hom = 0;
for (int i = 1; i < EM_N-1; i++)
{
//discovery_prior += 1e-3/(double)i;
}
//discovery_prior = Math.log10(discovery_prior);
//discovery_null_prior = Math.log10(1.0 - discovery_prior);
for (int i = 0; i < sample_names.size(); i++)
{
discovery_posterior += calls[i].pBest;
discovery_null += calls[i].pRef;
//System.out.printf("DBG %f %f %c %s\n", calls[i].pBest, calls[i].pRef, ref, calls[i].bases);
}
double discovery_lod = discovery_posterior - discovery_null;
if (discovery_lod == 0) { alt = 'N'; }
discovery_output_file.printf("%s %c %c %f %f %f %f\n", context.getLocation(), ref, alt, EM_alt_freq, discovery_posterior, discovery_null, discovery_lod);
if (calls[i].depth == 0) { continue; }
discovery_likelihood += calls[i].pBest;
discovery_null += calls[i].pRef;
//System.out.printf("DBG %f %f %c %s\n", calls[i].pBest, calls[i].pRef, ref, calls[i].bases);
if (calls[i].qhat == 0.0) { n_ref += 1; }
if (calls[i].qhat == 0.5) { n_het += 1; }
if (calls[i].qhat == 1.0) { n_hom += 1; }
}
double discovery_lod = (discovery_likelihood + discovery_prior) - (discovery_null + discovery_null_prior);
if (discovery_lod <= 0) { alt = 'N'; }
//discovery_output_file.printf("%s %c %c %f %f %f %f %f %f %d %d %d\n", context.getLocation(), ref, alt, EM_alt_freq, discovery_likelihood, discovery_null, discovery_prior, discovery_lod, EM_N, n_ref, n_het, n_hom);
AlleleFrequencyEstimate estimate = new AlleleFrequencyEstimate(context.getLocation(),
ref,
alt,
(int)EM_N,
EM_alt_freq,
EM_alt_freq,
discovery_lod,
0.0,
discovery_likelihood + discovery_prior,
discovery_null + discovery_prior,
context.getReads().size(),
(String)null,
(double[][])null,
(double[])null,
(String)null);
estimate.n_ref = n_ref; // HACK
estimate.n_het = n_het; // HACK
estimate.n_hom = n_hom; // HACK
return estimate;
for (int i = 0; i < sample_names.size(); i++)
{
ReadBackedPileup pileup = new ReadBackedPileup(ref, contexts[i]);
if (calls[i].depth == 0) { continue; }
//if (calls[i].lodVsRef < lodThreshold) { continue; }
//discovery_output_file.printf("%s %s %c %f %s %f %f %f %f %f %s\n", context.getLocation(), sample_names.get(i), ref, EM_alt_freq, calls[i].genotype(), calls[i].lodVsRef, calls[i].lodVsNextBest, calls[i].pBest, calls[i].pRef, discovery_lod, pileup.getBases());
}
//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)
@ -249,6 +306,25 @@ public class PoolCaller extends LocusWalker<AlleleFrequencyEstimate, String>
return new LocusContext(location, reads, offsets);
}
private LocusContext filterLocusContextByStrand(LocusContext context, String strand)
{
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);
// Filter for strandedness
if ((!strand.contains("+")) && (read.getReadNegativeStrandFlag() == false)) { continue; }
if ((!strand.contains("-")) && (read.getReadNegativeStrandFlag() == true)) { continue; }
reads.add(read);
offsets.add(offset);
}
return new LocusContext(context.getLocation(), reads, offsets);
}
private LocusContext[] filterLocusContext(LocusContext context, List<String> sample_names, int downsample)
{
HashMap<String,Integer> index = new HashMap<String,Integer>();
@ -315,9 +391,15 @@ public class PoolCaller extends LocusWalker<AlleleFrequencyEstimate, String>
return contexts;
}
private void CollectStrandInformation(char ref, LocusContext context)
{
List<SAMRecord> reads = context.getReads();
List<Integer> offsets = context.getOffsets();
}
public void onTraversalDone(String result)
{
System.out.printf("OTD\n");
try
{
discovery_output_file.flush();
@ -334,7 +416,7 @@ public class PoolCaller extends LocusWalker<AlleleFrequencyEstimate, String>
public String reduceInit()
{
discovery_output_file.printf("loc ref alt EM_alt_freq discovery_posterior discovery_null discovery_lod\n");
discovery_output_file.printf("loc ref alt EM_alt_freq discovery_likelihood discovery_null discovery_prior discovery_lod EM_N n_ref n_het n_hom fw_alt fw_lod bw_alt bw_lod\n");
for (int i = 0; i < callers.size(); i++)
{
callers.get(i).reduceInit();

30
java/src/org/broadinstitute/sting/playground/utils/AlleleFrequencyEstimate.java
View File

@ -35,6 +35,9 @@ public class AlleleFrequencyEstimate {
public double[][] quals;
public double[] posteriors;
public String sample_name;
public int n_ref;
public int n_het;
public int n_hom;
GenomeLoc l;
@ -42,11 +45,11 @@ public class AlleleFrequencyEstimate {
public AlleleFrequencyEstimate(GenomeLoc location, char ref, char alt, int N, double qhat, double qstar, double lodVsRef, double lodVsNextBest, double pBest, double pRef, int depth, String bases, double[][] quals, double[] posteriors, String sample_name)
{
if( Double.isNaN(lodVsRef)) { System.out.printf("%s: lodVsRef is NaN\n", location.toString()); }
if( Double.isNaN(lodVsNextBest)) { System.out.printf("lodVsNextBest is NaN\n"); }
if( Double.isNaN(qhat)) { System.out.printf("qhat is NaN\n"); }
if( Double.isNaN(qstar)) { System.out.printf("qstar is NaN\n"); }
if( Double.isNaN(pBest)) { System.out.printf("pBest is NaN\n"); }
if( Double.isNaN(pRef)) { System.out.printf("pRef is NaN (%c %s)\n", ref, bases); }
if( Double.isNaN(lodVsNextBest)) { System.out.printf("%s lodVsNextBest is NaN\n", location.toString()); }
if( Double.isNaN(qhat)) { System.out.printf("%s qhat is NaN\n", location.toString()); }
if( Double.isNaN(qstar)) { System.out.printf("%s qstar is NaN\n", location.toString()); }
if( Double.isNaN(pBest)) { System.out.printf("%s pBest is NaN\n", location.toString()); }
if( Double.isNaN(pRef)) { System.out.printf("%s pRef is NaN (%c %s)\n", location.toString(), ref, bases); }
if( Double.isInfinite(lodVsRef))
{
@ -206,6 +209,23 @@ public class AlleleFrequencyEstimate {
}
}
public String asPoolTabularString()
{
return String.format("%s %c %c %f %f %f %s %f %d %d %d %d",
location,
ref,
alt,
qstar,
pBest,
pRef,
"NA",
lodVsRef,
N,
n_ref,
n_het,
n_hom);
}
public double posterior()
{

27
java/src/org/broadinstitute/sting/playground/utils/GenotypeLikelihoods.java
View File

@ -81,8 +81,10 @@ public class GenotypeLikelihoods {
offNextBestBasePriors.put("TT", 0.505);
}
public void add(char ref, char read, byte qual) {
for (int i = 0; i < genotypes.length; i++) {
public void add(char ref, char read, byte qual)
{
for (int i = 0; i < genotypes.length; i++)
{
likelihoods[i] += calculateAlleleLikelihood(ref, read, genotypes[i], qual);
}
}
@ -96,14 +98,19 @@ public class GenotypeLikelihoods {
double p_base;
if ((h1 == h2) && (h1 == read)) {
p_base = getOneMinusQual(qual); //Math.log10(1 - p_error);
} else if ((h1 != h2) && (h1 == read) || (h2 == read)) {
p_base = getOneHalfMinusQual(qual); // )Math.log10(0.5 - (p_error / 2.0));
} else {
// the real math would be
// likelihood += log10(pow(10,(qual/-10.0)));
// but it simplifies to
if ((h1 == h2) && (h1 == read))
{
// hom
p_base = getOneMinusQual(qual);
}
else if ((h1 != h2) && ((h1 == read) || (h2 == read)))
{
// het
p_base = getOneHalfMinusQual(qual);
}
else
{
// error
p_base = qual/-10.0;
}