diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TileCovariate.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TileCovariate.java index a3affb22b..b02820581 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TileCovariate.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TileCovariate.java @@ -26,7 +26,7 @@ package org.broadinstitute.sting.gatk.walkers.recalibration; import org.broadinstitute.sting.utils.StingException; import net.sf.samtools.SAMRecord; -import edu.mit.broad.picard.illumina.parser.IlluminaUtil; +import net.sf.picard.util.IlluminaUtil; /** * @author alecw@broadinstitute.org diff --git a/packages/PicardPrivate.xml b/packages/PicardPrivate.xml index 20412c162..ebe26b2b1 100644 --- a/packages/PicardPrivate.xml +++ b/packages/PicardPrivate.xml @@ -7,7 +7,6 @@ - @@ -21,6 +20,7 @@ + diff --git a/settings/repository/edu.mit.broad/picard-private-parts-1377-sharding.jar b/settings/repository/edu.mit.broad/picard-private-parts-1409-sharding.jar similarity index 57% rename from settings/repository/edu.mit.broad/picard-private-parts-1377-sharding.jar rename to settings/repository/edu.mit.broad/picard-private-parts-1409-sharding.jar index 7ed9c6c8d..439153e5f 100644 Binary files a/settings/repository/edu.mit.broad/picard-private-parts-1377-sharding.jar and b/settings/repository/edu.mit.broad/picard-private-parts-1409-sharding.jar differ diff --git a/settings/repository/edu.mit.broad/picard-private-parts-1377-sharding.xml b/settings/repository/edu.mit.broad/picard-private-parts-1409-sharding.xml similarity index 55% rename from settings/repository/edu.mit.broad/picard-private-parts-1377-sharding.xml rename to settings/repository/edu.mit.broad/picard-private-parts-1409-sharding.xml index d434cb03d..3c2c86322 100644 --- a/settings/repository/edu.mit.broad/picard-private-parts-1377-sharding.xml +++ b/settings/repository/edu.mit.broad/picard-private-parts-1409-sharding.xml @@ -1,3 +1,3 @@ - + diff --git a/settings/repository/net.sf/picard-1.19.395-sharding.xml b/settings/repository/net.sf/picard-1.19.395-sharding.xml deleted file mode 100644 index 3608edd9c..000000000 --- a/settings/repository/net.sf/picard-1.19.395-sharding.xml +++ /dev/null @@ -1,3 +0,0 @@ - - - diff --git a/settings/repository/net.sf/picard-1.19.395-sharding.jar b/settings/repository/net.sf/picard-1.19.430-sharding.jar similarity index 76% rename from settings/repository/net.sf/picard-1.19.395-sharding.jar rename to settings/repository/net.sf/picard-1.19.430-sharding.jar index 6da7e63ae..836e02e70 100644 Binary files a/settings/repository/net.sf/picard-1.19.395-sharding.jar and b/settings/repository/net.sf/picard-1.19.430-sharding.jar differ diff --git a/settings/repository/net.sf/picard-1.19.430-sharding.xml b/settings/repository/net.sf/picard-1.19.430-sharding.xml new file mode 100644 index 000000000..d3a705294 --- /dev/null +++ b/settings/repository/net.sf/picard-1.19.430-sharding.xml @@ -0,0 +1,3 @@ + + + diff --git a/settings/repository/net.sf/sam-1.19.395-sharding.jar b/settings/repository/net.sf/sam-1.19.430-sharding.jar similarity index 76% rename from settings/repository/net.sf/sam-1.19.395-sharding.jar rename to settings/repository/net.sf/sam-1.19.430-sharding.jar index ebad98146..f80aadb6f 100644 Binary files a/settings/repository/net.sf/sam-1.19.395-sharding.jar and b/settings/repository/net.sf/sam-1.19.430-sharding.jar differ diff --git a/settings/repository/net.sf/sam-1.19.395-sharding.xml b/settings/repository/net.sf/sam-1.19.430-sharding.xml similarity index 52% rename from settings/repository/net.sf/sam-1.19.395-sharding.xml rename to settings/repository/net.sf/sam-1.19.430-sharding.xml index 9a5de6d8a..a6fb4a33b 100644 --- a/settings/repository/net.sf/sam-1.19.395-sharding.xml +++ b/settings/repository/net.sf/sam-1.19.430-sharding.xml @@ -1,3 +1,3 @@ - +