diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/BAMFileStat.java b/java/src/org/broadinstitute/sting/gatk/datasources/BAMFileStat.java index e7e2b65c6..90d9a5fad 100644 --- a/java/src/org/broadinstitute/sting/gatk/datasources/BAMFileStat.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/BAMFileStat.java @@ -80,6 +80,7 @@ public class BAMFileStat extends CommandLineProgram { } public void inspect(PrintStream outputStream, Integer startPosition, Integer stopPosition) { + /* outputStream.printf("Number of reference sequences: %d%n", this.referenceToBins.size()); for(int referenceSequence: referenceToBins.keySet()) { Bin[] bins = referenceToBins.get(referenceSequence); @@ -97,6 +98,7 @@ public class BAMFileStat extends CommandLineProgram { outputStream.printf("%d,",indexEntry); outputStream.printf("%n"); } + */ } } } diff --git a/settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-2.jar b/settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-3.jar similarity index 91% rename from settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-2.jar rename to settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-3.jar index 568416b9b..05ba590d3 100644 Binary files a/settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-2.jar and b/settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-3.jar differ diff --git a/settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-2.xml b/settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-3.xml similarity index 55% rename from settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-2.xml rename to settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-3.xml index 7beba5fb1..1b36b12ab 100644 --- a/settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-2.xml +++ b/settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-3.xml @@ -1,3 +1,3 @@ - + diff --git a/settings/repository/net.sf/picard-1.16.362-sharding.jar b/settings/repository/net.sf/picard-1.16.363-sharding.jar similarity index 95% rename from settings/repository/net.sf/picard-1.16.362-sharding.jar rename to settings/repository/net.sf/picard-1.16.363-sharding.jar index 8f28163ba..60f977b53 100644 Binary files a/settings/repository/net.sf/picard-1.16.362-sharding.jar and b/settings/repository/net.sf/picard-1.16.363-sharding.jar differ diff --git a/settings/repository/net.sf/picard-1.16.362-sharding.xml b/settings/repository/net.sf/picard-1.16.363-sharding.xml similarity index 76% rename from settings/repository/net.sf/picard-1.16.362-sharding.xml rename to settings/repository/net.sf/picard-1.16.363-sharding.xml index 8605edce7..31c6ab92b 100644 --- a/settings/repository/net.sf/picard-1.16.362-sharding.xml +++ b/settings/repository/net.sf/picard-1.16.363-sharding.xml @@ -1,3 +1,3 @@ - + diff --git a/settings/repository/net.sf/sam-1.16.362-sharding.jar b/settings/repository/net.sf/sam-1.16.363-sharding.jar similarity index 92% rename from settings/repository/net.sf/sam-1.16.362-sharding.jar rename to settings/repository/net.sf/sam-1.16.363-sharding.jar index ef72fa9cf..3ebadb087 100644 Binary files a/settings/repository/net.sf/sam-1.16.362-sharding.jar and b/settings/repository/net.sf/sam-1.16.363-sharding.jar differ diff --git a/settings/repository/net.sf/sam-1.16.362-sharding.xml b/settings/repository/net.sf/sam-1.16.363-sharding.xml similarity index 52% rename from settings/repository/net.sf/sam-1.16.362-sharding.xml rename to settings/repository/net.sf/sam-1.16.363-sharding.xml index 7692bcd7d..cc08fdd9e 100644 --- a/settings/repository/net.sf/sam-1.16.362-sharding.xml +++ b/settings/repository/net.sf/sam-1.16.363-sharding.xml @@ -1,3 +1,3 @@ - +