a lot of people have been asking me for the equivalent of the old "PrintCoverage" command from Arachne. Even though I show them the pileup, and they agree that's more accurate/complete, they don't want to modify their scripts and/or write a translator. It was simple enough to write, so here it is.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@863 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/playground/gatk/walkers/PrintCoverageWalker.java

@@ -0,0 +1,96 @@
+package org.broadinstitute.sting.playground.gatk.walkers;
+
+import net.sf.picard.reference.ReferenceSequence;
+import net.sf.samtools.Cigar;
+import net.sf.samtools.CigarElement;
+import net.sf.samtools.SAMRecord;
+import net.sf.samtools.util.StringUtil;
+import org.broadinstitute.sting.gatk.LocusContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
+import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
+import org.broadinstitute.sting.gatk.walkers.By;
+import org.broadinstitute.sting.gatk.walkers.DataSource;
+import org.broadinstitute.sting.gatk.walkers.LocusWalker;
+import org.broadinstitute.sting.playground.indels.SWPairwiseAlignment;
+import org.broadinstitute.sting.playground.utils.GenotypeLikelihoods;
+import org.broadinstitute.sting.utils.Pair;
+import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+@By(DataSource.REFERENCE)
+public class PrintCoverageWalker extends LocusWalker<Integer, Integer> {
+    public void initialize() {
+        out.println("chrom position reference a c g t");
+    }
+
+    public String walkerType() { return "ByLocus"; }
+
+    // Do we actually want to operate on the context?
+    public boolean filter(RefMetaDataTracker tracker, char ref, LocusContext context) {
+        return true;    // We are keeping all the reads
+    }
+
+    public Integer map(RefMetaDataTracker tracker, char ref, LocusContext context) {
+        int aCount = 0;
+        int cCount = 0;
+        int gCount = 0;
+        int tCount = 0;
+
+        char upRef = Character.toUpperCase(ref);
+
+        List<SAMRecord> reads = context.getReads();
+        for ( int i = 0; i < reads.size(); i++ )
+        {
+            SAMRecord read = reads.get(i);
+
+            if (read.getNotPrimaryAlignmentFlag() ||
+                read.getDuplicateReadFlag() ||
+                read.getReadUnmappedFlag() ||
+                read.getMappingQuality() <= 0
+                    ) {
+                continue;
+            }
+
+            int offset = context.getOffsets().get(i);
+            char base = read.getReadString().charAt(offset);
+            if (base == 'a' || base == 'A') { aCount++; }
+            if (base == 'c' || base == 'C') { cCount++; }
+            if (base == 'g' || base == 'G') { gCount++; }
+            if (base == 't' || base == 'T') { tCount++; }
+        }
+
+
+        out.printf("%s %d %s %d %d %d %d\n",
+                   context.getContig(),
+                   context.getPosition(),
+                   upRef,
+                   aCount,
+                   cCount,
+                   gCount,
+                   tCount);
+
+        return -1;
+    }
+
+
+    // Given result of map function
+    public Integer reduceInit() {
+        return 0;
+    }
+    public Integer reduce(Integer value, Integer sum) {
+        return value + sum;
+    }
+
+    @Override
+    public void onTraversalDone(Integer result) {
+    }
+
+
+}