zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Add -noVerbose flag to stop output of INFO data. 

Cuts runtime by 30% and output from 65Mb to 1Kb.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3591 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-06-18 18:53:35 +00:00
parent 724affc3cc
commit aa1852575e
1 changed files with 24 additions and 9 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

33
java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/HLACallerWalker.java
View File

@ -75,6 +75,9 @@ public class HLACallerWalker extends ReadWalker<Integer, Integer> {
@Argument(fullName = "HLAdictionary", shortName = "HLAdictionary", doc = "HLA dictionary file", required = true) @Argument(fullName = "HLAdictionary", shortName = "HLAdictionary", doc = "HLA dictionary file", required = true)
public String HLAdatabaseFile = "HLA_DICTIONARY.txt"; public String HLAdatabaseFile = "HLA_DICTIONARY.txt";
@Argument(fullName = "turnOffVerboseOutput", shortName = "noVerbose", doc = "Do not output verbose probability descriptions (INFO lines) ", required = false)
protected boolean NO_VERBOSE = false;
GATKArgumentCollection args = this.getToolkit().getArguments(); GATKArgumentCollection args = this.getToolkit().getArguments();
// Initializing variables // Initializing variables
@ -127,8 +130,10 @@ public class HLACallerWalker extends ReadWalker<Integer, Integer> {
AllelesToSearch = similarityReader.GetAllelesToSearch(); AllelesToSearch = similarityReader.GetAllelesToSearch();
AlleleCount = similarityReader.GetAlleleCount(); AlleleCount = similarityReader.GetAlleleCount();
LocusCount = similarityReader.GetLocusCount(); LocusCount = similarityReader.GetLocusCount();
for (int i = 0; i < AllelesToSearch.size(); i++){ if (!NO_VERBOSE) {
out.printf("INFO\tAllelesToSearch\t%s\t%s\n",AllelesToSearch.get(i),AlleleCount.get(AllelesToSearch.get(i))); for (int i = 0; i < AllelesToSearch.size(); i++){
out.printf("INFO\tAllelesToSearch\t%s\t%s\n",AllelesToSearch.get(i),AlleleCount.get(AllelesToSearch.get(i)));
}
} }
}else{ }else{
ReadsToDiscard = new ArrayList<String>(); ReadsToDiscard = new ArrayList<String>();
@ -155,7 +160,9 @@ public class HLACallerWalker extends ReadWalker<Integer, Integer> {
baseLikelihoods = baseLikelihoodsReader.GetBaseLikelihoods(); baseLikelihoods = baseLikelihoodsReader.GetBaseLikelihoods();
positions = baseLikelihoodsReader.GetPositions(); positions = baseLikelihoodsReader.GetPositions();
PolymorphicSites = baseLikelihoodsReader.GetPolymorphicSites(); PolymorphicSites = baseLikelihoodsReader.GetPolymorphicSites();
out.printf("INFO\t%s polymorphic sites found\n",PolymorphicSites.length); if (!NO_VERBOSE) {
out.printf("INFO\t%s polymorphic sites found\n",PolymorphicSites.length);
}
int l = PolymorphicSites.length; int l = PolymorphicSites.length;
SNPnumInRead = new int[l]; SNPnumInRead = new int[l];
@ -284,7 +291,9 @@ public class HLACallerWalker extends ReadWalker<Integer, Integer> {
Likelihoods.add(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); 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); Output.add(data);
out.printf("INFO\t%s\n",data); if (!NO_VERBOSE) {
out.printf("INFO\t%s\n",data);
}
if (DEBUG){ if (DEBUG){
} }
@ -424,7 +433,9 @@ public class HLACallerWalker extends ReadWalker<Integer, Integer> {
} }
out.print("\n"); out.print("\n");
} }
out.printf("INFO\t%s\t%s\t%s\t%.1f\t%.1f\t%.2f\t%.2f\t%.1f\t%.2f\t%.0f\t%.0f\t%.0f\t%.2f",s1[0],name1,name2,aLikelihood4/count,pLikelihood4/count,f1,f2,likelihood/count,prob,count1,count2,locusCount,accountedFor); if (!NO_VERBOSE) {
out.printf("INFO\t%s\t%s\t%s\t%.1f\t%.1f\t%.2f\t%.2f\t%.1f\t%.2f\t%.0f\t%.0f\t%.0f\t%.2f",s1[0],name1,name2,aLikelihood4/count,pLikelihood4/count,f1,f2,likelihood/count,prob,count1,count2,locusCount,accountedFor);
}
for (int i = 0; i < Populations.length; i++){ for (int i = 0; i < Populations.length; i++){
if (AlleleFrequencies[i].containsKey(s[0])){f1 = Double.valueOf(AlleleFrequencies[i].get(s[0]).toString());}else{f1=.000001;} if (AlleleFrequencies[i].containsKey(s[0])){f1 = Double.valueOf(AlleleFrequencies[i].get(s[0]).toString());}else{f1=.000001;}
if (AlleleFrequencies[i].containsKey(s[1])){f2 = Double.valueOf(AlleleFrequencies[i].get(s[1]).toString());}else{f2=.000001;} if (AlleleFrequencies[i].containsKey(s[1])){f2 = Double.valueOf(AlleleFrequencies[i].get(s[1]).toString());}else{f2=.000001;}
@ -583,7 +594,7 @@ private int GenotypeIndex(char a, char b){
index = GenotypeIndex(read1.charAt(pos-start1),read2.charAt(pos-start2)); index = GenotypeIndex(read1.charAt(pos-start1),read2.charAt(pos-start2));
if (index > -1){ if (index > -1){
likelihood = likelihood + baseLikelihoods[i][index]; likelihood = likelihood + baseLikelihoods[i][index];
if (debug){ if (!NO_VERBOSE || debug){
c1 = read1.charAt(pos-start1); c1 = read1.charAt(pos-start1);
c2 = read2.charAt(pos-start2); c2 = read2.charAt(pos-start2);
out.printf("INFO: DEBUG %s\t%s\t%s\t%s\t%s\t%s\t%.2f\n",HLAnames[a1],HLAnames[a2],pos,c1,c2,index,likelihood); out.printf("INFO: DEBUG %s\t%s\t%s\t%s\t%s\t%s\t%.2f\n",HLAnames[a1],HLAnames[a2],pos,c1,c2,index,likelihood);
@ -747,9 +758,11 @@ private int GenotypeIndex(char a, char b){
for (Map.Entry<String, Double> entry : entries) { for (Map.Entry<String, Double> entry : entries) {
if (num <= Math.max(5,entries.size()/8)){ if (num <= Math.max(5,entries.size()/8)){
AllelesToSearch.add(entry.getKey()); AllelesToSearch.add(entry.getKey());
out.printf("INFO\t%s\t%.2f\t%.2f\n",entry.getKey(),entry.getValue(),Phase2Digit.get(entry.getKey())); if (!NO_VERBOSE) {
out.printf("INFO\t%s\t%.2f\t%.2f\n",entry.getKey(),entry.getValue(),Phase2Digit.get(entry.getKey()));
}
num++; num++;
}else{ }else if (!NO_VERBOSE) {
if (!AllelesToSearch.contains(entry.getKey())){ if (!AllelesToSearch.contains(entry.getKey())){
out.printf("INFO\t%s\t%.2f\t%.2f\tNotSearched\n",entry.getKey(),entry.getValue(),Phase2Digit.get(entry.getKey())); out.printf("INFO\t%s\t%.2f\t%.2f\tNotSearched\n",entry.getKey(),entry.getValue(),Phase2Digit.get(entry.getKey()));
}else{ }else{
@ -758,7 +771,9 @@ private int GenotypeIndex(char a, char b){
} }
} }
out.printf("INFO\n"); if (!NO_VERBOSE) {
out.printf("INFO\n");
}
} }
} }
} }