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- update picard, sam, variants and tribble after fixing bug in BCF2Ut…

…ils.makeDictionary as reported in ticket 52571227

- update call for VCFSimpleHeaderLine constructor in GATKVCFUtils
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commit 0f5bb706ffd3e02a2fec45f32317f29e4e45cb6d 1 parent ec0c338
@amilev amilev authored
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2  public/java/src/org/broadinstitute/sting/utils/variant/GATKVCFUtils.java
@@ -75,7 +75,7 @@ public static VCFHeaderLine getCommandLineArgumentHeaderLine(final GenomeAnalysi
attributes.put("Date", date.toString());
attributes.put("Epoch", Long.toString(date.getTime()));
attributes.put("CommandLineOptions", engine.createApproximateCommandLineArgumentString(argumentSources.toArray()));
- return new VCFSimpleHeaderLine(GATK_COMMAND_LINE_KEY, attributes, Collections.<String>emptyList());
+ return new VCFSimpleHeaderLine(GATK_COMMAND_LINE_KEY, attributes);
}
public static <T extends Feature> Map<String, VCFHeader> getVCFHeadersFromRods(GenomeAnalysisEngine toolkit, List<RodBinding<T>> rodBindings) {
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BIN  ...gs/repository/net.sf/picard-1.96.1525.jar → ...gs/repository/net.sf/picard-1.96.1534.jar
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2  ...gs/repository/net.sf/picard-1.96.1525.xml → ...gs/repository/net.sf/picard-1.96.1534.xml
@@ -1,3 +1,3 @@
<ivy-module version="1.0">
- <info organisation="net.sf" module="picard" revision="1.96.1525" status="release" />
+ <info organisation="net.sf" module="picard" revision="1.96.1534" status="release" />
</ivy-module>
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3  settings/repository/net.sf/sam-1.96.1525.xml
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
- <info organisation="net.sf" module="sam" revision="1.96.1525" status="release" />
-</ivy-module>
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BIN  settings/repository/net.sf/sam-1.96.1525.jar → settings/repository/net.sf/sam-1.96.1534.jar 100755 → 100644
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3  settings/repository/net.sf/sam-1.96.1534.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+ <info organisation="net.sf" module="sam" revision="1.96.1534" status="release" />
+</ivy-module>
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BIN  ...epository/org.broad/tribble-1.96.1526.jar → ...epository/org.broad/tribble-1.96.1534.jar
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2  ...epository/org.broad/tribble-1.96.1526.xml → ...epository/org.broad/tribble-1.96.1534.xml
@@ -1,3 +1,3 @@
<ivy-module version="1.0">
- <info organisation="org.broad" module="tribble" revision="1.96.1526" status="integration" />
+ <info organisation="org.broad" module="tribble" revision="1.96.1534" status="integration" />
</ivy-module>
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BIN  .../org.broadinstitute/variant-1.96.1525.jar → .../org.broadinstitute/variant-1.96.1534.jar
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2  .../org.broadinstitute/variant-1.96.1525.xml → .../org.broadinstitute/variant-1.96.1534.xml
@@ -1,3 +1,3 @@
<ivy-module version="1.0">
- <info organisation="org.broadinstitute" module="variant" revision="1.96.1525" status="integration" />
+ <info organisation="org.broadinstitute" module="variant" revision="1.96.1534" status="integration" />
</ivy-module>
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