3dc4d3c3a9
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
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removed the auto-deletion of the reflections jar, and removed the very old OmniPlan document we had checked-in.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4056 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-19 00:42:37 +00:00
24e81e3e7b
moved to wiki
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1292 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-22 16:35:23 +00:00
045d74d09c
Cleanup my pathetic prose.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1263 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-15 21:35:13 +00:00
a04f205a7f
GATK readme.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1262 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-15 21:00:08 +00:00
f5b00c20d0
Updated python files
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1182 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-07 14:15:39 +00:00
891f4c2bd9
up on the wiki, removing it from the repo. Ignore my last commit
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1141 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-01 15:42:02 +00:00
05c5659053
This document is now up as content on the wiki, so I'm removing it from svn.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1140 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-01 15:40:32 +00:00
74e9bb46b4
Contents of the Hello World doc are now in the wiki.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1137 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-30 22:32:56 +00:00
fdff233d70
new injector args and address Kiran's question
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1134 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-30 19:49:22 +00:00
455275996f
Added contents to the wiki.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1131 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-30 18:29:46 +00:00
fe421e5712
All IntelliJ best practices info is now on the wiki.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1128 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-30 16:45:52 +00:00
74cc7136f7
All info from the user manual is now in the wiki. Deleting.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1124 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-30 15:29:59 +00:00
3bacb3db03
updated some defaults
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1114 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-26 19:28:05 +00:00
da1f168a3e
updated docs
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1110 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-26 05:20:17 +00:00
f6eeb36c93
updated doc
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1092 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 14:32:51 +00:00
6b5560e1e9
Fairly detailed first pass at a README for the MSA realigner
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1075 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-23 01:54:38 +00:00
5440dd13df
Preparation for point release of read calibrator: no artificial heap size limit, no duplicate dbsnp records.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@986 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 18:39:33 +00:00
e77dfe9983
Allow script to be easily modified to support different platforms.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@955 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-09 16:06:57 +00:00
127c321d0a
Cut over to 1kG version of fasta / reference. Updated doc with latest version of tool summary.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@940 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-08 21:11:44 +00:00
f6e985d97f
Documentation for read quality recalibrator. We have to spend some time rethinking how to organize these mini-releases.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@938 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-08 16:54:39 +00:00
5f924c46e0
Added documentation for calling the GATK from Matlab. This is to document the extreme basic and experimental support for using Matlab to call the GATK, and is more of a placeholder for when we have time to revisit supporting this.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@687 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-13 15:25:51 +00:00
6ecc43f385
Provide a default logger, some config settings, and some doc updates.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@557 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-29 02:06:05 +00:00
ef4a107548
Updated the hello world document to reflect system changes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@499 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-22 23:25:15 +00:00
1660379753
Matt's current status.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@466 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-17 18:03:11 +00:00
01d000411d
added some updates to the omniplan
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@465 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-17 17:44:04 +00:00
820cf09198
Updated with last week / next week for 6 April.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@299 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-06 14:05:20 +00:00
edc44807af
rod's now have names. Use getName() to access it. Next step is better interface to accessing rods
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@286 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-03 16:41:33 +00:00
24e8581c30
Slight improvements to allele caller interface; fixed problem with printing progress
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@260 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-02 16:44:12 +00:00
7ce280723f
Updated todo list
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@251 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-01 20:31:42 +00:00
d37d81822d
Fixed the Hello, World doc to reflect the collapse in the walker hierarchy.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@238 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-31 15:23:29 +00:00
8e2ba7a294
Added more detail to documentation based on the feedback I've been getting
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on command-line arguments.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@237 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-31 15:21:05 +00:00
8be02f6a34
Check in the omniplan file for easier sharing.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@228 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-30 21:31:54 +00:00
20e650f397
Added examples that can be cut and pasted.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@227 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-30 19:05:44 +00:00
1d972969a9
A dumping ground for information that will eventually become the GATK user manual. Currently has basic information about command-line arguments and walker output streams.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@223 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-30 16:04:30 +00:00
9840a089ef
Added documentation for our coding standards.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@193 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-25 19:42:09 +00:00
09d605bb37
Changed how the example walker gets run, I'm about to check in the GNU style command line args.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@143 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-22 20:10:17 +00:00
6fdd622160
Describe how GATK finds walkers. Change the example to avoid copying the class file into the walkers directory.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@104 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-19 22:41:12 +00:00
41fec1565c
Hello, world! for GATK.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@101 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-19 21:46:22 +00:00
3ac3592ee4
IntelliJ cleanup. Added docs on build environment.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@61 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-16 15:26:34 +00:00
feb70ff627
Added instructions for 3rd party sources and remote debugging.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@59 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-16 01:29:48 +00:00
28d1e33e3b
Added description of available ant tasks, help using intellij on Linux.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@58 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-16 00:03:55 +00:00
45d69397b7
Added the beginnings of a guide to integrating our code with Intellij
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@49 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-13 18:44:13 +00:00
aaron
ebanks
hanna
depristo