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

Nicer reporting functions. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@678 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-05-12 19:48:30 +00:00
parent ee99320c83
commit 57ecb7fbf1
1 changed files with 55 additions and 2 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

57
java/src/org/broadinstitute/sting/playground/gatk/walkers/ContrastiveGenotypers.java
View File

@ -56,8 +56,8 @@ public class ContrastiveGenotypers extends LocusWalker<Integer, Integer> {
ref = Character.toUpperCase(ref);
rodGFF hmi = getHapmapInfo(tracker);
boolean isInDbSNP = isInDbSNP(tracker);
/*
if (hmi != null) {
ReadBackedPileup pileup = new ReadBackedPileup(ref, context);
String bases = pileup.getBases();
@ -81,7 +81,6 @@ public class ContrastiveGenotypers extends LocusWalker<Integer, Integer> {
}
}
}
*/
AlleleFrequencyEstimate call_1b = caller_1b.map(tracker, ref, context);
AlleleFrequencyEstimate call_4b = caller_4b.map(tracker, ref, context);
@ -90,6 +89,36 @@ public class ContrastiveGenotypers extends LocusWalker<Integer, Integer> {
// printDebuggingInfo(ref, context, call_1b, call_4b, hmi, System.out);
//}
String calltype_1b = "homref";
if (isHet(call_1b)) { calltype_1b = "het"; }
if (isHomNonRef(call_1b)) { calltype_1b = "homnonref"; }
String calltype_4b = "homref";
if (isHet(call_4b)) { calltype_4b = "het"; }
if (isHomNonRef(call_4b)) { calltype_4b = "homnonref"; }
ReadBackedPileup pileup = new ReadBackedPileup(ref, context);
String bases = pileup.getBases();
String bases2 = pileup.getSecondaryBasePileup();
out.printf("%s %c %s %s %4.4f %4.4f %s %s %4.4f %4.4f %b %b %s %s %s\n",
context.getLocation().toString(),
ref,
calltype_1b,
call_1b.genotype(),
call_1b.lodVsRef,
call_1b.lodVsNextBest,
calltype_4b,
call_4b.genotype(),
call_4b.lodVsRef,
call_4b.lodVsNextBest,
isInDbSNP,
hmi != null,
(hmi != null) ? hmi.getFeature() : "NN",
bases,
bases2
);
caller_1b.metrics.nextPosition(call_1b, tracker);
caller_4b.metrics.nextPosition(call_4b, tracker);
@ -133,6 +162,24 @@ public class ContrastiveGenotypers extends LocusWalker<Integer, Integer> {
return hapmap_chip_genotype;
}
private boolean isInDbSNP(RefMetaDataTracker tracker) {
boolean is_dbSNP_SNP = false;
for ( ReferenceOrderedDatum datum : tracker.getAllRods() )
{
if ( datum != null )
{
if ( datum instanceof rodDbSNP)
{
rodDbSNP dbsnp = (rodDbSNP)datum;
if (dbsnp.isSNP()) is_dbSNP_SNP = true;
}
}
}
return is_dbSNP_SNP;
}
private void printDebuggingInfo(char ref, LocusContext context, AlleleFrequencyEstimate call_1b, AlleleFrequencyEstimate call_4b, rodGFF hmi, PrintStream lout) {
ReadBackedPileup pileup = new ReadBackedPileup(ref, context);
@ -220,5 +267,11 @@ public class ContrastiveGenotypers extends LocusWalker<Integer, Integer> {
);
}
System.out.print("1-Base Metrics");
caller_1b.metrics.printMetricsAtLocusIntervals(1);
System.out.print("4-Base Metrics");
caller_4b.metrics.printMetricsAtLocusIntervals(1);
System.out.println("--------------");
}
}