gatk-3.8

Commit Graph

Author	SHA1	Message	Date
kshakir	860b172ef1	Defaulting the MFCP to run without a tear script. Added a missing virtual output for the inner FCP, so that Queue can tell a run of the FCP is dot-done. Enabled the MCFPTest for the first time, running without the tear script. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5264 348d0f76-0448-11de-a6fe-93d51630548a	2011-02-17 21:13:14 +00:00
kshakir	d185c2961f	Added pipeline for calling FCP in batches called MultiFullCallingPipeline. Bug smashes for the MCFP: Synchronized access to LSF library and modifications to the QGraph. If values are missing from the graph with -run make sure to exit with a non-zero. Refactored QGraph to pre-generate a unique Int for each QNode speeding up getHashCode/equals inside the graph. Added jobPriority and removed jobLimitSeconds from QFunction. All scatter gather is by default in a single sub directory queueScatterGather. Moved some FCPTest into BaseTest/PipelineTest for use by MFCPTest. Rev'ed the 1000G bams used for validation from v1 to v2 and added code to look for the bams before running other tests. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5247 348d0f76-0448-11de-a6fe-93d51630548a	2011-02-15 18:26:14 +00:00

Author

SHA1

Message

Date

kshakir

860b172ef1

Defaulting the MFCP to run without a tear script.

Added a missing virtual output for the inner FCP, so that Queue can tell a run of the FCP is dot-done.
Enabled the MCFPTest for the first time, running without the tear script.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5264 348d0f76-0448-11de-a6fe-93d51630548a

2011-02-17 21:13:14 +00:00

kshakir

d185c2961f

Added pipeline for calling FCP in batches called MultiFullCallingPipeline.

Bug smashes for the MCFP:
  Synchronized access to LSF library and modifications to the QGraph.
  If values are missing from the graph with -run make sure to exit with a non-zero.
  Refactored QGraph to pre-generate a unique Int for each QNode speeding up getHashCode/equals inside the graph.
  Added jobPriority and removed jobLimitSeconds from QFunction.
  All scatter gather is by default in a single sub directory queueScatterGather.
  Moved some FCPTest into BaseTest/PipelineTest for use by MFCPTest.
  Rev'ed the 1000G bams used for validation from v1 to v2 and added code to look for the bams before running other tests.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5247 348d0f76-0448-11de-a6fe-93d51630548a

2011-02-15 18:26:14 +00:00

2 Commits (7ffcade3c3bd2d28e875dc443a22e061104d1612)