gatk-3.8

gatk3的最后一个经典版本3.8

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delangel b03055099a a) Changed the way we classify and log indel events (e.g. in IndelClasses table inside IndelStatistics VE module). Made names clearer, and split logging of event length with number of repetitions of event. b) Add an experimental annotation to log indel type string inside the INFO field, just for debugging/temp analysis purposes (will consider making it standard if it proves useful). git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5424 348d0f76-0448-11de-a6fe-93d51630548a		2011-03-11 17:37:41 +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	a) Changed the way we classify and log indel events (e.g. in IndelClasses table inside IndelStatistics VE module). Made names clearer, and split logging of event length with number of repetitions of event.	2011-03-11 17:37:41 +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	One last little thing, I swear	2011-03-11 17:37:40 +00:00
ruby	accidentally commited an old tool	2010-08-25 15:42:02 +00:00
scala	Updated LSF libraries to use Pointer instead of Structure.ByReference for struct arrays since the the latter is autoRead() and LSF doesn't always return null for empty arrays.	2011-03-10 22:58:54 +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	Small bug fixes:	2011-03-10 19:54:14 +00:00
ivy.xml	Added commons math, for Kristian.	2011-02-14 18:57:21 +00:00