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
f64f3e2d90
Phase II support for generic reference order data set parsing.
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Can read GFF and dbSNP files correctly.
Traversal engine now supports keeping moving window of reference ordered data along with the locus iterator.
Tested by walking through a sam file keeping track of the dbSNP positions encountered -- they definitely look right...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@13 348d0f76-0448-11de-a6fe-93d51630548a
2009-02-28 20:47:48 +00:00
dee840efa5
Moved out of java/src
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@12 348d0f76-0448-11de-a6fe-93d51630548a
2009-02-28 17:52:34 +00:00
69e9a467d0
Wrong directory
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@11 348d0f76-0448-11de-a6fe-93d51630548a
2009-02-28 17:52:16 +00:00
bd1fadd9fe
Validating walker for lots of bam files
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@10 348d0f76-0448-11de-a6fe-93d51630548a
2009-02-28 17:05:08 +00:00
e892c3fd98
Shouldn't be in the tree
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@9 348d0f76-0448-11de-a6fe-93d51630548a
2009-02-28 15:31:17 +00:00
17aabb38f9
Basic reorganization of tree
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@8 348d0f76-0448-11de-a6fe-93d51630548a
2009-02-28 15:28:56 +00:00
c9f0161e24
Initial support for reference ordered data sets
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@7 348d0f76-0448-11de-a6fe-93d51630548a
2009-02-27 17:07:57 +00:00
bb55947e2e
Better organization of AnalysisTK modules
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6 348d0f76-0448-11de-a6fe-93d51630548a
2009-02-26 22:15:41 +00:00
5e3adc76fc
Initial Analysis toolkit
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5 348d0f76-0448-11de-a6fe-93d51630548a
2009-02-26 21:50:51 +00:00
59083a47d5
Initial Analysis toolkit
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4 348d0f76-0448-11de-a6fe-93d51630548a
2009-02-26 21:50:29 +00:00
aaron
hanna
depristo
andrewk
jmaguire