151c37591e
removed unnecessary import that produced a warning. where did it come from in the first place??
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@80 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-17 15:46:27 +00:00
478425b3d8
Better error messages
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@79 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-17 15:37:02 +00:00
0fd55d91d2
Fixed bug in unsafe mode
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@78 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-17 15:28:04 +00:00
c74bd871b1
added module for aligned reads
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@77 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-17 14:08:54 +00:00
28cc670a92
Walker to print out a histogram of aligned reads per mismatches allowed
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@76 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-17 14:05:29 +00:00
9ae551e858
Lots of error checking added, fixed bugs associated with reading files out of order, added support for U (unsafe) flag for processing reads
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@75 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-16 23:22:04 +00:00
36b8b34490
Main tool that builds the clusters (multiple alignments) - so far; to be heavily refactored; most methods should find their proper homes in other classes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@74 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-16 22:03:31 +00:00
b9ffcdf047
matrix as the name suggests; utilizes special property (zeros at diagonal and below) to use less memory at the expense of slower access; this one is built directly on primitive data type (double) so it should not have any overhead associated with java classes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@73 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-16 22:01:53 +00:00
a17ed3cbf1
this class really computes (and keeps) a gapless pairwise alignment between the two sequences, ILT-style
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@72 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-16 21:59:26 +00:00
4972b03059
a class that keeps a pile of reads and can perform some simple computations on them; does not perform multiple alignments (so far) - external tools do the job
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@71 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-16 21:58:05 +00:00
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
02dec23628
Set of classes that perform clustering of reads without regard for the reference; at this stage the code actually knows nothing about 'indels' despite the package name; kept in a separate project-specific package for now - a playground within a playground
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@65 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-16 21:51:13 +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
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
asivache
depristo
ebanks
hanna
andrewk
aaron