object or by a single object and all the references it contains. Requires a command-line change to add a Java agent to
the command-line; see the Sizeof.java javadoc for details.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3889 348d0f76-0448-11de-a6fe-93d51630548a
Modified build script so that queue is cleaned during "ant clean".
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3611 348d0f76-0448-11de-a6fe-93d51630548a
Current version only has syntatic sugar for accessing the graph via rules ex. "bam" -> "bam.bai", "samtools index ${bam}" and DOES NOT have sugar for constructing your own graph.
Usage info on the internal wiki at https://iwww.broadinstitute.org/gsa/wiki/index.php/Queue
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3420 348d0f76-0448-11de-a6fe-93d51630548a
IMPORTANT: it was really redundant that we had -Dsingle and -Dsingleintegration to run single unit tests and integration tests, now you can just use -Dsingle to run a single test for performance, unit, and integration tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3136 348d0f76-0448-11de-a6fe-93d51630548a
for test compatibility, but not sure whether we still need this feature. TODO: Poll the group about this feature.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2949 348d0f76-0448-11de-a6fe-93d51630548a
won't aren't impacted when building the GATK from outside the base directory.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2696 348d0f76-0448-11de-a6fe-93d51630548a
more like a resource bundle at this point, changed it over to use the Java ResourceBundle
support classes.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2606 348d0f76-0448-11de-a6fe-93d51630548a
feedback received. Also, add a flag to build.xml to disable generation of
docs on demand (use ant -Ddisable.doc=true to disable docs).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2284 348d0f76-0448-11de-a6fe-93d51630548a
in GenomeAnalysisTK.jar. Still no support for actually displaying the archived javadoc. Also change the approach
to providing package javadocs: retired the deprecated package.html file in favor of Java1.5-style package-info.java.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2263 348d0f76-0448-11de-a6fe-93d51630548a
You can tell ant not to halt with: 'ant -Dhalt=no' (yes is the default)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2240 348d0f76-0448-11de-a6fe-93d51630548a
Hopefully this is a temporary solution and these classes will be migrated
into picard-public.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2041 348d0f76-0448-11de-a6fe-93d51630548a
A couple of notes:
-Commented out BaseTransitionTableCalculator.scala because it's won't build; Chris could you fix this one (or kill it if it's not needed).
-Removed the PrintReadsScala walker; moved the code over to a ScalaCountLoci walker (which is what the code was really doing).
-Added configurations items to the ivy xml file.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1956 348d0f76-0448-11de-a6fe-93d51630548a
-Bamboo will now run the integration tests once a day, and the normal units tests on each check-in.
-Also added a bunch of unit tests for VariantEval walker
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1555 348d0f76-0448-11de-a6fe-93d51630548a
out how do deal with the playground jar.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1344 348d0f76-0448-11de-a6fe-93d51630548a
ant -Ddist=altDist
or
ant -Ddist=/where/you/want/jars
Also changed the test build to depend on playground build instead of core, right now tests fail if you only build the core.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1299 348d0f76-0448-11de-a6fe-93d51630548a
hanna
aaron
kshakir
kiran
depristo
jmaguire
rpoplin