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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%
R 0.2%
JavaScript 0.1%
 
 
 
 
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chartl b089d35b21 Fix expand intervals to do the right thing: 
- No more duplicate intervals
 - Truncation at intervals that already exist, e.g.

exists:      |--------|           |-------|
new:               |---------|
fixed:                 |-----|

note that weird instances like:

exists:           |-|        |-|                  |-|
new:           |---------------------|
fixed:                          |----|

e.g. you're truncated to the nearest interval on whatever side. In general many behaviors could happen in this instance, this is the one currently implemented.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5323 348d0f76-0448-11de-a6fe-93d51630548a
 		2011-02-26 04:19:01 +00:00
R Now says FNR, not FDR. We really need to clean up VQSR 2011-02-15 12:28:09 +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 Don't do genotype concordance on comp tracks without genotypes, even if they have an AC 2011-02-25 21:11:50 +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 If you scatter depth of coverage and need to do something more sophisticated than gathering up (e.g. concatenating) the interval summary file, and need to smartly gather up a full summary file, modify (stress on MODIFY) this script to do it 2011-02-25 01:23:53 +00:00
ruby accidentally commited an old tool 2010-08-25 15:42:02 +00:00
scala Fix expand intervals to do the right thing: 2011-02-26 04:19:01 +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