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Another formatting change to make Hapmap sites more clearly visible. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1004 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-06-12 19:53:21 +00:00
parent 811f560efb
commit 0583459839
1 changed files with 7 additions and 0 deletions
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7
java/src/org/broadinstitute/sting/gatk/walkers/PileupWithContextWalker.java
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@ -4,6 +4,7 @@ import org.broadinstitute.sting.gatk.LocusContext;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.refdata.rodDbSNP; import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.rodGFF;
import org.broadinstitute.sting.utils.cmdLine.Argument; import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.utils.ReadBackedPileup; import org.broadinstitute.sting.utils.ReadBackedPileup;
import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.Utils;
@ -80,9 +81,15 @@ public class PileupWithContextWalker extends LocusWalker<Integer, Integer> imple
String rodString = ""; String rodString = "";
for ( ReferenceOrderedDatum datum : tracker.getAllRods() ) { for ( ReferenceOrderedDatum datum : tracker.getAllRods() ) {
/*
if ( datum != null && ! (datum instanceof rodDbSNP)) { if ( datum != null && ! (datum instanceof rodDbSNP)) {
rodString += datum.toSimpleString() + " "; rodString += datum.toSimpleString() + " ";
} }
*/
if ( datum != null && (datum instanceof rodGFF)) {
rodString += "Hapmap: " + datum.toSimpleString() + " ";
}
} }
rodDbSNP dbsnp = (rodDbSNP)tracker.lookup("dbSNP", null); rodDbSNP dbsnp = (rodDbSNP)tracker.lookup("dbSNP", null);