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

This commit is contained in:
Mark DePristo 2011-10-05 17:12:09 -07:00
parent a91509e7dd 6d6149b9a2
commit b068846407
2 changed files with 5 additions and 7 deletions
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10
build.xml
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@ -547,12 +547,10 @@
<target name="vcf.jar" depends="gatk.compile,init.jar"> <target name="vcf.jar" depends="gatk.compile,init.jar">
<jar jarfile="${dist.dir}/vcf.jar"> <jar jarfile="${dist.dir}/vcf.jar">
<fileset dir="${java.classes}"> <classfileset dir="${java.classes}">
<include name="**/utils/codecs/**/*.class"/> <rootfileset dir="${java.classes}" includes="org/broadinstitute/sting/utils/codecs/vcf/**/*.class" />
<include name="**/utils/variantcontext/**/*.class"/> <rootfileset dir="${java.classes}" includes="org/broadinstitute/sting/utils/variantcontext/**/*.class" />
<include name="org/broadinstitute/sting/utils/exceptions/**"/> </classfileset>
<include name="org/broadinstitute/sting/utils/help/DocumentedGATKFeature.class"/>
</fileset>
</jar> </jar>
</target> </target>

2
public/R/src/gsalib/R/gsa.read.gatkreport.R
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@ -99,5 +99,5 @@ gsa.read.gatkreport <- function(filename) {
.gsa.assignGATKTableToEnvironment(tableName, tableHeader, tableRows, tableEnv); .gsa.assignGATKTableToEnvironment(tableName, tableHeader, tableRows, tableEnv);
} }
gatkreport = as.list(tableEnv); gatkreport = as.list(tableEnv, all.names=TRUE);
} }