6d481c64e7
just a square matrix of arbitrary stuff; the stuff must be full fledged Java type, however, not a primitive type. Hooray Java!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@70 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-16 21:56:45 +00:00
c68e0cc1fe
Walks along the sequence and emits a sequence of subsequent, encoded Kmers (uses short int, so currently it's up to K=8)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@68 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-16 21:54:45 +00:00
34d9af4702
Remove orphaned modules directory.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@67 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-16 21:53:05 +00:00
1e89dbfcb1
Sequence bundled with its Kmer-based lookup index (same thing as old lookup table)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@66 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-16 21:52:57 +00:00
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
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
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
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
asivache
hanna
andrewk
depristo
ebanks
aaron