685fc8bd61
Partial implementation of single sample allele calling
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@64 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-16 19:30:42 +00:00
4808dff110
Added latest snapshot of picard.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@63 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-16 19:05:14 +00:00
8ccbcc4101
Mismatch counter
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@62 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-16 15:51:48 +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
3b5003bd11
Added support for accessing the reference in read traversal
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@60 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-16 14:46:19 +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
d93e9613f4
fixes to build.xml
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@57 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-15 22:46:43 +00:00
69aa669928
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@56 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-15 22:42:24 +00:00
01e950ef2f
Reference ordered data files
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@55 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-15 22:37:20 +00:00
24ae381c97
Renaming of ATK to GATK, the genome analysis TK.
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Also added several more layers of error checking
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@54 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-15 22:23:25 +00:00
c9cb7a3596
Renaming of ATK to GATK, the genome analysis TK.
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Also added several more layers of error checking
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@53 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-15 22:21:48 +00:00
a38a038204
fixed spelling mistake of method
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@52 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-13 18:51:53 +00:00
968281e460
fixed spelling mistake of method
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@51 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-13 18:50:29 +00:00
c33a779f33
corrected spelling of method
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@50 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-13 18:48:11 +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
a2ff12ee06
Add javadoc task. Lots of work remaining to get clean generation of javadoc w/o warnings.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@48 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-13 18:43:07 +00:00
09307f768c
Fix for leniency actually working
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@47 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-13 16:26:18 +00:00
10427f8191
Bad merge has been fixed!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@46 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-13 16:00:23 +00:00
2a8dc05f2e
Support for threaded IO!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@45 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-13 14:50:45 +00:00
851254970c
First somewhat functional version of AlleleFrequency caller!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@44 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-13 04:10:43 +00:00
7c7d4b3a95
Added support for HangingLocusIterator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@43 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-12 23:31:00 +00:00
04befb942e
Added support for HangingLocusIterator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@42 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-12 23:30:19 +00:00
8a63606e11
Add publication date to Picard jar.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@41 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-12 21:23:30 +00:00
727822f0c1
Add debugging info to executables.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@40 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-12 20:04:00 +00:00
4ab1fa249b
Simplification and commenting.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@39 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-11 22:58:22 +00:00
4af5e54411
Replay changes that were obliterated by the move.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@38 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-11 21:43:31 +00:00
c3f74f46c4
Oops! Restore changes that were clobbered during the move.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@37 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-11 21:26:29 +00:00
ec8a555cae
Added a dependency on JUnit to the playground
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@36 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-11 21:21:07 +00:00
5031875507
Move to new directory organization.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@35 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-11 20:58:01 +00:00
25ddc0f5ea
Skeleton of new directory structure.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@34 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-11 20:05:05 +00:00
6a0a45950e
First swipe at autogeneration of the classpath.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@33 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-11 19:44:02 +00:00
3c605e95cb
First inklings of a unified allele caller!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@32 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-11 17:54:24 +00:00
150610d63d
Move to ivy for dependency management.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@31 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-11 17:14:04 +00:00
393400deea
Documented TraveralEngine
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@30 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-10 22:09:12 +00:00
716af47dd5
Added NullWalker module (do nothing).
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Added SingleSampleGenotyper module (old-school single sample genotyping).
Added Utils.SortPermutation (return the permutaton that would sort the input array).
Added Utils.PermuteArray (apply a permutation to an array).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@29 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-10 21:26:07 +00:00
6b8650b0c0
Patch up scripts to use new directory structure.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@28 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-10 19:54:46 +00:00
ea0a826f8f
Clean up 3rd party dependencies.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@27 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-10 19:34:00 +00:00
e4bde58353
Fix for inaccurate and misleading timing information, now only prints estimated time to completion when the location flag isn't set
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@25 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-10 14:59:42 +00:00
17c94a8c5c
make build.xml work from within the java directory.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@24 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-06 22:58:12 +00:00
e938dbda47
Check for the existence of the module name and return error rather than throwing an exception if not found.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@23 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-04 00:15:35 +00:00
a81a1bdbb4
Minor bug fixed to progress meter
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@22 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-02 22:19:39 +00:00
851e1df072
reconciled TraversalEngine
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@21 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-02 21:51:25 +00:00
46c3f1a0ac
Support for progress tracking during parsing of SAM files.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@20 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-02 21:49:08 +00:00
49a84c965e
Added basic GenomeLoc class
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Support for operating on any location in genome (albeit slowly)
Improvements to dbSNP support
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@19 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-02 18:18:48 +00:00
63f8d82e36
Fix for ROD in TraversalEngine
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@18 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-02 02:46:34 +00:00
b19e4b502b
Continuing to expand support for ROD. These edits add a program, PrepareROD, that sorts and prepares RODs for consumption by the analysis TK.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@17 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-01 23:32:23 +00:00
fd447d7c1d
Renamed Empty to Count methods in analysisTK
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@16 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-01 23:31:33 +00:00
a5c76f7666
Renamed Empty to Count methods in analysisTK
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@15 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-01 23:31:23 +00:00
0ee2375292
Working on reference ordered data; added build.xml for ant!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@14 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-01 18:27:32 +00:00
andrewk
hanna
depristo
ebanks
aaron
jmaguire