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Added option to only consider alleles of > specific allele frequency. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3557 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
sjia 2010-06-15 02:09:35 +00:00
parent 8a895f481f
commit b99a5e06f3
1 changed files with 46 additions and 43 deletions
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89
java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/HLACallerWalker.java
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@ -60,8 +60,8 @@ public class HLACallerWalker extends ReadWalker<Integer, Integer> {
@Argument(fullName = "useInterval", shortName = "useInterval", doc = "Use only these intervals in phase calculation", required = false) @Argument(fullName = "useInterval", shortName = "useInterval", doc = "Use only these intervals in phase calculation", required = false)
public String IntervalsFile = ""; public String IntervalsFile = "";
@Argument(fullName = "onlyfrequent", shortName = "onlyfrequent", doc = "Only consider alleles with frequency > 0.0001", required = false) @Argument(fullName = "minFreq", shortName = "minFreq", doc = "only consider alleles greater than this frequency", required = false)
public boolean ONLYFREQUENT = false; public double minFrequency = 0.0;
@Argument(fullName = "maxAllowedMismatches", shortName = "maxAllowedMismatches", doc = "Max number of mismatches tolerated per read (default 7)", required = false) @Argument(fullName = "maxAllowedMismatches", shortName = "maxAllowedMismatches", doc = "Max number of mismatches tolerated per read (default 7)", required = false)
public int MAXALLOWEDMISMATCHES = 6; public int MAXALLOWEDMISMATCHES = 6;
@ -208,7 +208,7 @@ public class HLACallerWalker extends ReadWalker<Integer, Integer> {
public void onTraversalDone(Integer numreads) { public void onTraversalDone(Integer numreads) {
String name1, name2, d4_name1, d4_name2, d2_name1, d2_name2; String name1, name2, d4_name1, d4_name2, d2_name1, d2_name2;
Double frq1 = 0.0, frq2 = 0.0, log1 = 0.0, log2 = 0.0,alleleLikelihood= 0.0, phaseLikelihood=0.0, minfrq = 0.0, likelihood = 0.0; Double frq1 = 0.0, frq2 = 0.0, log1 = 0.0, log2 = 0.0,alleleLikelihood= 0.0, phaseLikelihood=0.0, likelihood = 0.0;
int numCombinations = 0; int numCombinations = 0;
//For debugging specific alleles //For debugging specific alleles
@ -223,10 +223,6 @@ public class HLACallerWalker extends ReadWalker<Integer, Integer> {
} }
} }
if (ONLYFREQUENT){
minfrq = 0.0001;
}
double max; double max;
ArrayList Output = new ArrayList<String>(); ArrayList Output = new ArrayList<String>();
ArrayList Likelihoods = new ArrayList<Double>(); ArrayList Likelihoods = new ArrayList<Double>();
@ -240,7 +236,7 @@ public class HLACallerWalker extends ReadWalker<Integer, Integer> {
String [] n1 = name1.split("\\*"); String [] n1 = name1.split("\\*");
d4_name1 = n1[0] + "*" + n1[1].substring(0, 4); d4_name1 = n1[0] + "*" + n1[1].substring(0, 4);
d2_name1 = n1[0] + "*" + n1[1].substring(0, 2); d2_name1 = n1[0] + "*" + n1[1].substring(0, 2);
if (AllelesToSearch.contains(d4_name1)){// || CommonAlleles.contains(d4_name1) if (AllelesToSearch.contains(d4_name1)){
if (MaxFrequencies.containsKey(d4_name1)){ if (MaxFrequencies.containsKey(d4_name1)){
frq1 = Double.parseDouble(MaxFrequencies.get(d4_name1).toString()); frq1 = Double.parseDouble(MaxFrequencies.get(d4_name1).toString());
@ -248,44 +244,51 @@ public class HLACallerWalker extends ReadWalker<Integer, Integer> {
if (n1[1].length() > 4){if (n1[1].substring(4, 5).equals("N")){frq1 = .00000005;}else{frq1 = .000001;}}else{frq1 = .000001;} if (n1[1].length() > 4){if (n1[1].substring(4, 5).equals("N")){frq1 = .00000005;}else{frq1 = .000001;}}else{frq1 = .000001;}
} }
// Allele 2 if (frq1 > minFrequency){
// Allele 2
for (int j = i; j < HLAnames.length; j++){ for (int j = i; j < HLAnames.length; j++){
name2 = HLAnames[j].substring(4); name2 = HLAnames[j].substring(4);
String [] n2 = name2.split("\\*"); String [] n2 = name2.split("\\*");
d4_name2 = n2[0] + "*" + n2[1].substring(0, 4); d4_name2 = n2[0] + "*" + n2[1].substring(0, 4);
d2_name2 = n2[0] + "*" + n2[1].substring(0, 2); d2_name2 = n2[0] + "*" + n2[1].substring(0, 2);
if (n1[0].equals(n2[0]) && (AllelesToSearch.contains(d4_name2))){// || CommonAlleles.contains(d4_name2) if (n1[0].equals(n2[0]) && (AllelesToSearch.contains(d4_name2))){
if (MaxFrequencies.containsKey(d4_name2)){ if (MaxFrequencies.containsKey(d4_name2)){
frq2 = Double.parseDouble(MaxFrequencies.get(d4_name2).toString()); frq2 = Double.parseDouble(MaxFrequencies.get(d4_name2).toString());
}else{ }else{
if (n2[1].length() > 4){if (n2[1].substring(4, 5).equals("N")){frq2 = .00000005;}else{frq2 = .000001;}}else{frq2 = .000001;} if (n2[1].length() > 4){if (n2[1].substring(4, 5).equals("N")){frq2 = .00000005;}else{frq2 = .000001;}}else{frq2 = .000001;}
}
//Calculate allele and phase likelihoods for each allele pair
alleleLikelihood = CalculateAlleleLikelihood(i,j,HLAreads,false);
numCombinations++;
//If there is data at the allele pair, continue with other calculations
if (alleleLikelihood < 0){
phaseLikelihood = CalculatePhaseLikelihood(i,j,false,false);
log1=Math.log10(frq1);
log2=Math.log10(frq2);
//sum likelihoods
likelihood = alleleLikelihood+phaseLikelihood+log1+log2;
if (!MaxLikelihoods.containsKey(n1[0])){MaxLikelihoods.put(n1[0], likelihood);}
if (likelihood > (Double) MaxLikelihoods.get(n1[0])) {
MaxLikelihoods.put(n1[0], likelihood);
} }
Likelihoods.add(likelihood);
String data = String.format("%s\t%s\t%s\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f",n1[0],name1,name2,alleleLikelihood,phaseLikelihood,log1,log2,likelihood); if (frq2 > minFrequency){
Output.add(data);
out.printf("INFO\t%s\n",data);
if (DEBUG){
//Calculate allele and phase likelihoods for each allele pair
alleleLikelihood = CalculateAlleleLikelihood(i,j,HLAreads,false);
numCombinations++;
//If there is data at the allele pair, continue with other calculations
if (alleleLikelihood < 0){
phaseLikelihood = CalculatePhaseLikelihood(i,j,false,false);
log1=Math.log10(frq1);
log2=Math.log10(frq2);
//sum likelihoods
likelihood = alleleLikelihood+phaseLikelihood+log1+log2;
if (!MaxLikelihoods.containsKey(n1[0])){MaxLikelihoods.put(n1[0], likelihood);}
if (likelihood > (Double) MaxLikelihoods.get(n1[0])) {
MaxLikelihoods.put(n1[0], likelihood);
}
Likelihoods.add(likelihood);
String data = String.format("%s\t%s\t%s\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f",n1[0],name1,name2,alleleLikelihood,phaseLikelihood,log1,log2,likelihood);
Output.add(data);
out.printf("INFO\t%s\n",data);
if (DEBUG){
}
}
} }
} }
} }