diff --git a/playground/java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java b/core/java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java similarity index 100% rename from playground/java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java rename to core/java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java diff --git a/playground/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java b/core/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java similarity index 72% rename from playground/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java rename to core/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java index a895849c6..8b7b2f670 100644 --- a/playground/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java +++ b/core/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java @@ -27,27 +27,16 @@ public class PileupWalker extends BasicLociWalker { // Map over the org.broadinstitute.sting.gatk.LocusContext public Integer map(List rodData, char ref, LocusContext context) { - //System.out.printf("Reads %s:%d %d%n", context.getContig(), context.getPosition(), context.getReads().size()); - //for ( SAMRecord read : context.getReads() ) { - // System.out.println(" -> " + read.getReadName()); - //} - List reads = context.getReads(); List offsets = context.getOffsets(); String bases = ""; String quals = ""; - //String offsetString = ""; for ( int i = 0; i < reads.size(); i++ ) { SAMRecord read = reads.get(i); int offset = offsets.get(i); - //if ( offset >= read.getReadString().length() ) - // System.out.printf(" [%2d] [%s] %s%n", offset, read.format(), read.getReadString()); - bases += read.getReadString().charAt(offset); quals += read.getBaseQualityString().charAt(offset); - //offsetString += i; - //System.out.printf(" [%2d] [%s] %s%n", offset, read.getReadString().charAt(offset), read.getReadString()); } String rodString = ""; @@ -55,7 +44,6 @@ public class PileupWalker extends BasicLociWalker { if ( datum != null ) { if ( datum instanceof rodDbSNP) { rodDbSNP dbsnp = (rodDbSNP)datum; - //System.out.printf(" DBSNP %s on %s => %s%n", dbsnp.toSimpleString(), dbsnp.strand, Utils.join("/", dbsnp.getAllelesFWD())); rodString += dbsnp.toMediumString(); } else { @@ -70,9 +58,6 @@ public class PileupWalker extends BasicLociWalker { System.out.printf("%s: %s %s %s %s%n", context.getLocation(), ref, bases, quals, rodString); } - //for ( int offset : context.getOffsets() ) { - // System.out.println(" -> " + read.getReadName()); - //} return 1; } diff --git a/playground/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java b/core/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java similarity index 100% rename from playground/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java rename to core/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java