- bsub command line is no longer fully printed out.
- extraBsubArgs hack is now a callback function updateJobRun.
Updated FullCallingPipelineTest to reflect latest changes to fullCallingPipeline.q.
Added a pipeline that tests the UGv2 runtimes at different bam counts and memory limits.
Updated VE packages that live in oneoffs to compile to oneoffs.
Added a hack to replace the deprecated symbol environ in Mac OS X 10.5+ which is needed by LSF7 on Mac.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4816 348d0f76-0448-11de-a6fe-93d51630548a
and the data backing it up deleted without my knowledge. Unfortunately, since the data was deleted, I had
to regenerate the data and a new md5. Hopefully the aligner output is still correct.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2493 348d0f76-0448-11de-a6fe-93d51630548a
checked in. Add a better way to write out unmapped reads (thanks Kiran!) Add
a pre-built version of the shared library to the repository for early adoption.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2111 348d0f76-0448-11de-a6fe-93d51630548a
the aligner base classes. Hack the managed implementation to support the
new interface.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2103 348d0f76-0448-11de-a6fe-93d51630548a
needs to plumbed through and it may leak memory.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2095 348d0f76-0448-11de-a6fe-93d51630548a
into JDK exceptions whenever possible instead of random core dumps. Don't
allow negative values for most of the 'bwa aln' input parameters.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2049 348d0f76-0448-11de-a6fe-93d51630548a
partitioned from the Java aligner, and both are partitioned from the more general-
purpose BWT reader.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2045 348d0f76-0448-11de-a6fe-93d51630548a
against a static library that the bwa compile (now) generates.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1980 348d0f76-0448-11de-a6fe-93d51630548a
ref genome. Make sure the reference genome is cached.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1961 348d0f76-0448-11de-a6fe-93d51630548a
the read bases to undo a previous read base reverse that doesn't occur in the
libbwa codepath.
Also fixed some memory management issues.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1938 348d0f76-0448-11de-a6fe-93d51630548a
handsake
kshakir
hanna