Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable

public/packages/PicardPrivate.xml

@@ -12,15 +12,12 @@
       <class name="edu.mit.broad.picard.variation.KnownVariantCodecV2" />
       <class name="edu.mit.broad.picard.variation.KnownVariantCodec" />
       <class name="edu.mit.broad.picard.variation.KnownVariantFileHeader" />
-      <class name="edu.mit.broad.picard.variation.GenerateDbSnpFile" />
       <class name="edu.mit.broad.picard.variation.VariantType" />
       <class name="edu.mit.broad.picard.variation.ObsoleteKnownVariantCodecV1" />
       <class name="edu.mit.broad.picard.variation.AbstractKnownVariantCodec" />
       <class name="edu.mit.broad.picard.variation.KnownVariantIterator" />
       <class name="edu.mit.broad.picard.variation.KnownVariantCodecFactory" />
       <class name="edu.mit.broad.picard.variation.KnownVariant" />
-      <class name="edu.mit.broad.picard.variation.DbSnpFileReader" />
-      <class name="edu.mit.broad.picard.variation.DbSnpFileGenerator" />
       <class name="net.sf.picard.util.IlluminaUtil" />
       <class name="edu.mit.broad.picard.genotype.fingerprint.v2.FingerprintingSummaryMetrics" />
       <class name="edu.mit.broad.picard.genotype.concordance.DbSnpMatchMetrics" />

settings/repository/edu.mit.broad/picard-private-parts-2125.xml

@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="edu.mit.broad" module="picard-private-parts" revision="2068" status="integration" publication="20111024162900" />
+    <info organisation="edu.mit.broad" module="picard-private-parts" revision="2125" status="integration" publication="20111024162900" />
 </ivy-module>

settings/repository/net.sf/picard-1.55.985.xml

@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="picard" revision="1.55.985" status="release" />
-</ivy-module>

settings/repository/net.sf/picard-1.57.1030.xml

@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="picard" revision="1.57.1030" status="release" />
+</ivy-module>

settings/repository/net.sf/sam-1.55.985.xml

@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="sam" revision="1.55.985" status="release" />
-</ivy-module>

settings/repository/net.sf/sam-1.57.1030.xml

@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="sam" revision="1.57.1030" status="release" />
+</ivy-module>