diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java index 32dcd1b0e..c5efe3df6 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java @@ -45,6 +45,16 @@ public class CoverageUtils { return String.format("%s_rg_%s",r.getSample(),r.getReadGroupId()); } else if ( type == DoCOutputType.Partition.library ) { return r.getLibrary(); + } else if ( type == DoCOutputType.Partition.center ) { + return r.getSequencingCenter(); + } else if ( type == DoCOutputType.Partition.platform ) { + return r.getPlatform(); + } else if ( type == DoCOutputType.Partition.sample_by_center ) { + return String.format("%s_cn_%s",r.getSample(),r.getSequencingCenter()); + } else if ( type == DoCOutputType.Partition.sample_by_platform) { + return String.format("%s_pl_%s",r.getSample(),r.getPlatform()); + } else if ( type == DoCOutputType.Partition.sample_by_platform_by_center ) { + return String.format("%s_pl_%s_cn_%s",r.getSample(),r.getPlatform(),r.getSequencingCenter()); } else { throw new StingException("Invalid type ID sent to getTypeID. This is a BUG!"); } diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java index 6846bafe4..edf142aaf 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java @@ -205,6 +205,26 @@ public class DepthOfCoverageWalker extends LocusWalker