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Suppressed emission of duplicate paths through a four-base pileup. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@498 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-04-22 21:08:45 +00:00
parent 6cef8bd76c
commit a3a1c9dae8
1 changed files with 20 additions and 7 deletions
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27
java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java
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@ -201,7 +201,8 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
} }
output_paths.add(best_path); output_paths.add(best_path);
output_likelihoods.add(best_likelihood); output_likelihoods.add(best_likelihood);
String s = ""; for (int j = 0; j < best_path.length; j++) { s += best_path[j]; } //String s = ""; for (int j = 0; j < best_path.length; j++) { s += best_path[j]; }
String s = ""; for (int j = 0; j < best_path.length; j++) { s += BaseUtils.baseIndexToSimpleBase(best_path[j]); }
done_paths.put(s,true); done_paths.put(s,true);
// 2. Enumerate all paths one-away from the best path // 2. Enumerate all paths one-away from the best path
@ -219,8 +220,14 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
path[i] = ref; path[i] = ref;
likelihood = best_likelihood - Math.log10(probs[i][alt]) + Math.log10(probs[i][ref]); likelihood = best_likelihood - Math.log10(probs[i][alt]) + Math.log10(probs[i][ref]);
} }
paths.add(path);
likelihoods.add(likelihood); //s = ""; for (int j = 0; j < path.length; j++) { s += path[j]; }
s = ""; for (int j = 0; j < path.length; j++) { s += BaseUtils.baseIndexToSimpleBase(path[j]); }
//if (!done_paths.containsKey(s)) {
paths.add(path);
likelihoods.add(likelihood);
//}
} }
// 3. Sort paths by likelihood // 3. Sort paths by likelihood
@ -233,11 +240,17 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
// 4. Choose the next best path // 4. Choose the next best path
int[] next_best_path = paths.get(paths.size()-1); int[] next_best_path = paths.get(paths.size()-1);
double next_best_likelihood = likelihoods.get(likelihoods.size()-1); double next_best_likelihood = likelihoods.get(likelihoods.size()-1);
s = ""; for (int j = 0; j < next_best_path.length; j++) { s += BaseUtils.baseIndexToSimpleBase(next_best_path[j]); }
if (done_paths.containsKey(s)) { break; }
output_paths.add(next_best_path); output_paths.add(next_best_path);
output_likelihoods.add(next_best_likelihood); output_likelihoods.add(next_best_likelihood);
paths.remove(paths.size()-1); paths.remove(paths.size()-1);
likelihoods.remove(likelihoods.size()-1); likelihoods.remove(likelihoods.size()-1);
s = ""; for (int j = 0; j < next_best_path.length; j++) { s += next_best_path[j]; }
//s = ""; for (int j = 0; j < next_best_path.length; j++) { s += next_best_path[j]; }
done_paths.put(s,true); done_paths.put(s,true);
/* /*
@ -263,9 +276,9 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
likelihood = next_best_likelihood - Math.log10(probs[i][alt]) + Math.log10(probs[i][ref]); likelihood = next_best_likelihood - Math.log10(probs[i][alt]) + Math.log10(probs[i][ref]);
} }
s = ""; //s = ""; for (int j = 0; j < path.length; j++) { s += path[j]; }
for (int j = 0; j < path.length; j++) { s += path[j]; } s = ""; for (int j = 0; j < path.length; j++) { s += BaseUtils.baseIndexToSimpleBase(path[j]); }
if (done_paths.get(s) == null) if (!done_paths.containsKey(s))
{ {
paths.add(path); paths.add(path);
likelihoods.add(likelihood); likelihoods.add(likelihood);