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gatk3的最后一个经典版本3.8
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Java 95.8%
Scala 3.8%
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kshakir 92045ecaa6 Finally figured out what data in the LSF C API call lsb_readjobinfo is causing JNA to SIGSEGV with a strlen error: 
- LSF recycles memory for C arrays, but sets a separate variable setting the size of the array to zero.
- JNA only sees the non-NULL pointer and starts to auto-access it, sometimes causing a SIGSEGV.
- In the short term neutered the jobInfoEnt structure so that this bad array is not autoRead().

QGraph updates:
- Job status is now checked in bulk every 30 seconds instead of one job at a time, even in the middle of dispatching jobs.
- If there is a hiccup (unexpected but not fatal error) during status check then the the error is ignored and status is checked again 30 seconds later.
- Jobs prefer to dispatch depth vs. breadth first.

More refactoring of SG framework separating the reusable code from the implementations.
The DistributedScatterFunction is still a work in progress and is not enabled yet. Still need to think through how Queue handles when a job dies.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5387 348d0f76-0448-11de-a6fe-93d51630548a
 		2011-03-07 04:29:06 +00:00
R Misc changes 2011-02-26 15:35:49 +00:00
analysis/depristo Scripts to create the GATK IAM user and give him/her rights to PutObject (and only PutObject) into the S3 storage instance. Updated the GATKRunReport to now upload using the GATK user, not mark@depristo.com. Running with -et AWS_S3 sends run reports up to the Amazon S3 cloud now. Going to request a few external users try this option so we can see it running at scale. I'm sure S3 can handle a few hundred thousand 1Kb uploads per days, though 2011-01-31 03:48:33 +00:00
archive Moving GLF code to archive 2011-01-15 22:42:42 +00:00
c Bug fixes for the bwa aligner and changes to support compiling against newer releases of the bwa code base. 2010-12-17 14:49:15 +00:00
doc removing the custom reflections library from the libs, and adding a release version. Hopefully this will fix the problem Menachem has been seeing with random JVM crashes. Also 2010-08-19 00:42:37 +00:00
java Finally figured out what data in the LSF C API call lsb_readjobinfo is causing JNA to SIGSEGV with a strlen error: 2011-03-07 04:29:06 +00:00
lua forgot to remove a debug line. 2011-02-15 16:25:48 +00:00
matlab Another matlab script -- this time for making power and coverage plots over a specific gene region. Lots of fun file reading, string manipulation, and exploration of the set() function 2009-11-30 20:02:25 +00:00
packages Adding the native jna support libraries from the jna.jar to the Queue package jar. 2011-01-08 10:48:30 +00:00
perl 2 more scripts I found helpful in syncing (and cleaning up) the 1000G mirror 2011-02-22 04:17:36 +00:00
python Minor utility improvements 2011-02-26 15:36:26 +00:00
ruby accidentally commited an old tool 2010-08-25 15:42:02 +00:00
scala Finally figured out what data in the LSF C API call lsb_readjobinfo is causing JNA to SIGSEGV with a strlen error: 2011-03-07 04:29:06 +00:00
settings Update Picard / sam-jdk at Tim's request. 2011-01-03 02:17:25 +00:00
shell While generating YAML now warning and skipping TSV rows that don't have all values. 2011-02-25 20:50:03 +00:00
testdata ReplaceReadGroups. Fixes BAM files without read group info. MissingReadGroup points people to this tool now. Please point users on the forum to this tool now. Will migrate to Picard. 2011-02-21 14:02:41 +00:00
LICENSE Adding a license to the root directory in case BOSC checks for one. Has the 2010-04-20 16:04:29 +00:00
build.xml fixed problem with Matt re: packaging commands from external walker codebases 2011-02-24 21:11:38 +00:00
ivy.xml Added commons math, for Kristian. 2011-02-14 18:57:21 +00:00