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clean-up of the GATK paper genotyper, and better output formatting for the simple call format we emit. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2529 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2010-01-06 20:54:56 +00:00
parent 7e3e714d3c
commit 576594eda2
2 changed files with 25 additions and 17 deletions
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35
java/src/org/broadinstitute/sting/playground/gatk/walkers/papergenotyper/GATKPaperGenotyper.java
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@ -16,17 +16,19 @@ import java.io.PrintStream;
/**
* A simple Bayesian genotyper, that outputs a text based call format. Intended to be used only as an
* example in the GATK publication.
*
* @author aaron
* @help.summary A simple, naive Bayesian genotyper that is used as an example locus walker in the GATK paper. THIS IS NOT TO BE USED FOR ANY ANALYSIS
*/
public class GATKPaperGenotyper extends LocusWalker<SimpleCall, Integer> implements TreeReducible<Integer> {
// the possible diploid genotype strings
private static enum GENOTYPE { AA, AC, AG, AT, CC, CG, CT, GG, GT, TT }
// where to write the genotyping data to
@Argument(fullName = "call_location", shortName = "cl", doc = "File to which calls should be written", required = true)
public PrintStream outputStream;
private PrintStream outputStream;
@Argument(fullName = "log_odds_score", shortName = "LOD", doc = "The LOD threshold for us to call confidently a genotype", required = false)
private double LODScore = 3.0;
/**
* our map function, which takes the reads spanning this locus, any associated reference ordered data,
@ -44,30 +46,33 @@ public class GATKPaperGenotyper extends LocusWalker<SimpleCall, Integer> impleme
double likelihoods[] = DiploidGenotypePriors.getReferencePolarizedPriors(ref.getBase(),
DiploidGenotypePriors.HUMAN_HETEROZYGOSITY,
DiploidGenotypePriors.PROB_OF_TRISTATE_GENOTYPE);
// get the bases and qualities from the pileup
byte bases[] = pileup.getBases();
byte quals[] = pileup.getQuals();
// for each genotype, determine it's likelihood value
for (GENOTYPE genotype : GENOTYPE.values())
for (int index = 0; index < bases.length; index++) {
if (quals[index] > 0) {
// our epsilon is the de-Phred scored base quality
double epsilon = Math.pow(10, quals[index] / -10.0);
byte pileupBase = bases[index];
for (char genotypeBase : genotype.toString().toCharArray()) {
double p = genotypeBase == pileupBase ? 1 - epsilon : epsilon / 3;
likelihoods[genotype.ordinal()] += Math.log10(p / 2);
}
double p = 0;
for (char r : genotype.toString().toCharArray())
p += r == pileupBase ? 1 - epsilon : epsilon / 3;
likelihoods[genotype.ordinal()] += Math.log10(p / genotype.toString().length());
}
}
Integer sortedList[] = Utils.SortPermutation(likelihoods);
// get our reference genotype
String refGenotype = (String.valueOf(ref.getBase()) + String.valueOf(ref.getBase())).toUpperCase();
// create call using the best genotype (GENOTYPE.values()[sortedList[9]].toString())
// and calculate the LOD score from best - ref (likelihoods[sortedList[9]] - likelihoods[sortedList[8])
// and calculate the LOD score from best - next best (9 and 8 in the sorted list, since the best likelihoods are closest to zero)
return new SimpleCall(context.getLocation(),
GENOTYPE.values()[sortedList[9]].toString(),
likelihoods[sortedList[9]] - likelihoods[GENOTYPE.valueOf(refGenotype).ordinal()]);
likelihoods[sortedList[9]] - likelihoods[sortedList[8]],
ref.getBase());
}
/**
@ -80,14 +85,16 @@ public class GATKPaperGenotyper extends LocusWalker<SimpleCall, Integer> impleme
}
/**
* Reduces a single map with the accumulator provided as the ReduceType.
* Reduces a single map with the accumulator provided as the ReduceType. We filter out calls,
* first making sure that the call is != null, secondly that the LOD score is above a moderate
* threshold (in this case 3).
*
* @param value result of the map.
* @param sum accumulator for the reduce.
* @return accumulator with result of the map taken into account.
*/
public Integer reduce(SimpleCall value, Integer sum) {
if (value != null) outputStream.println(value.toString());
if (value != null && value.LOD > LODScore) outputStream.println(value.toString());
return sum + 1;
}

7
java/src/org/broadinstitute/sting/playground/gatk/walkers/papergenotyper/SimpleCall.java
View File

@ -15,14 +15,15 @@ class SimpleCall {
public String genotype;
public double LOD;
public GenomeLoc loc;
SimpleCall(GenomeLoc location, String gt, double lod) {
public char ref;
SimpleCall(GenomeLoc location, String gt, double lod, char reference) {
genotype = gt;
LOD = lod;
loc = location;
this.ref = reference;
}
public String toString() {
return String.format("%s : %s with LOD %.4f", loc, genotype, LOD);
return String.format("%s\t%s\t%.4f\t%c", loc, genotype, LOD,ref);
}
}