diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCallingExperiment.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCallingExperiment.java new file mode 100644 index 000000000..a20650d50 --- /dev/null +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCallingExperiment.java @@ -0,0 +1,50 @@ + +package org.broadinstitute.sting.playground.gatk.walkers; + +import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; +import org.broadinstitute.sting.gatk.refdata.rodDbSNP; +import org.broadinstitute.sting.gatk.refdata.rodGFF; +import org.broadinstitute.sting.gatk.walkers.LocusWalker; +import org.broadinstitute.sting.gatk.LocusContext; +import org.broadinstitute.sting.playground.gatk.walkers.AlleleFrequencyWalker; +import org.broadinstitute.sting.playground.utils.AlleleFrequencyEstimate; +import org.broadinstitute.sting.utils.cmdLine.Argument; + +import java.util.List; + +public class PoolCallingExperiment extends LocusWalker +{ + List deep_callers; + List shallow_callers; + AlleleFrequencyWalker pooled_caller; + + @Argument public int DOWNSAMPLE; + + public AlleleFrequencyEstimate map(List rodData, char ref, LocusContext context) + { + for (int i = 0; i < context.getReads().size(); i++) + { + String read_group = (String)(context.getReads().get(i).getAttribute("RG")); + String sample = context.getReads().get(i).getHeader().getReadGroup(read_group).READ_GROUP_SAMPLE_TAG; + System.out.println("RG: " + read_group + " SAMPLE: " + sample); + } + return null; + } + + public void onTraversalDone() + { + return; + } + + public String reduceInit() + { + return ""; + } + + public String reduce(AlleleFrequencyEstimate alleleFreq, String sum) + { + return ""; + } + + +}