gatk-3.8

Author	SHA1	Message	Date
kshakir	e9c6f681a4	Instead of the pipeline's cleaner only writing BAMs with the target intervals, now pulling the list of contigs from the target intervals and outputing reads in those contigs. Added a brute force -retry <count> option to Queue for transient errors. Waiting up to 2 minutes for the LSF logs to appear before trying to display the errors from the logs. Updates to the local job runner error logging when a job fails. Refactored QGraph's settings as duplicate code was getting out of control. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4563 348d0f76-0448-11de-a6fe-93d51630548a	2010-10-22 22:22:30 +00:00
kshakir	b954a5a4d5	- After removing special code for intervals, instead of being of type File they are generated as List[File]. Changed previous checkin that was appending to this list and instead assigning a singleton list. - More cleanup including removing the temporary classes and intermediate error files. Quieting any errors using Apache Commons IO 2.0. - Counting the contigs during the QScript generation instead of the end user having to pass a separate contig interval list. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4539 348d0f76-0448-11de-a6fe-93d51630548a	2010-10-21 06:37:28 +00:00
kshakir	88a0d77433	Changed parsing engine to store the order the argument bindings based on their definition in the class, moving "-T" to the front of Queue command lines. Queue GATK generated .intervals is now a List(File) again removing special case handling in the generator. Instead of using @Scatter annotation, using ScatterFunction instance to determine if a job can be scattered. Implemented special VcfGatherFunction which only uses the header from the first file, even if the other files differ in their headers. Added a -deleteIntermediates to Queue to delete the outputs from intermediate commands after a successful run. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4536 348d0f76-0448-11de-a6fe-93d51630548a	2010-10-20 21:43:52 +00:00

Author

SHA1

Message

Date

kshakir

Instead of the pipeline's cleaner only writing BAMs with the target intervals, now pulling the list of contigs from the target intervals and outputing reads in those contigs.

Added a brute force -retry <count> option to Queue for transient errors.
Waiting up to 2 minutes for the LSF logs to appear before trying to display the errors from the logs.
Updates to the local job runner error logging when a job fails.
Refactored QGraph's settings as duplicate code was getting out of control.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4563 348d0f76-0448-11de-a6fe-93d51630548a

2010-10-22 22:22:30 +00:00

kshakir

b954a5a4d5

- After removing special code for intervals, instead of being of type File they are generated as List[File]. Changed previous checkin that was appending to this list and instead assigning a singleton list.

- More cleanup including removing the temporary classes and intermediate error files.  Quieting any errors using Apache Commons IO 2.0.
- Counting the contigs during the QScript generation instead of the end user having to pass a separate contig interval list.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4539 348d0f76-0448-11de-a6fe-93d51630548a

2010-10-21 06:37:28 +00:00

kshakir

88a0d77433

Changed parsing engine to store the order the argument bindings based on their definition in the class, moving "-T" to the front of Queue command lines.

Queue GATK generated .intervals is now a List(File) again removing special case handling in the generator.
Instead of using @Scatter annotation, using ScatterFunction instance to determine if a job can be scattered.
Implemented special VcfGatherFunction which only uses the header from the first file, even if the other files differ in their headers.
Added a -deleteIntermediates to Queue to delete the outputs from intermediate commands after a successful run.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4536 348d0f76-0448-11de-a6fe-93d51630548a

2010-10-20 21:43:52 +00:00

3 Commits (cbce3e3c83c72a8c7dff7b8fec00f00a2b419e83)