hanna
|
282f1d88b8
|
Make the operation 'read from the iterator and place on the queue' atomic with respect to hasNext(), next().
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@513 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-23 20:16:26 +00:00 |
aaron
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8c13940c5a
|
A lot of changes to support by-read sharding and some from debugging of the by loci traversals
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@511 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-23 19:03:14 +00:00 |
|
hanna
|
3d7575bbb8
|
Oops...omitted walker.initialize().
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@504 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-23 17:35:28 +00:00 |
|
hanna
|
1bf4d040d8
|
Increase default shard size from 5 to 100000.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@494 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-22 18:29:44 +00:00 |
|
hanna
|
3af66a462e
|
Make PrintLocusContextWalker less verbose.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@493 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-22 18:28:02 +00:00 |
|
hanna
|
4cafb95be8
|
TraverseByLoci / TraverseByLociByReference suffered from the same sam-triggered off-by-one (?) bug as TraverseByReference; it was just less obvious here because these versions don't shard.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@491 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-22 15:48:20 +00:00 |
kcibul
|
cb2f621d01
|
reverting accidental commit of change to shard size
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@490 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-22 00:33:28 +00:00 |
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kcibul
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b820130dce
|
* added ability to load multiple BAM files from command line
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@489 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-22 00:28:08 +00:00 |
kiran
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5abfc7d079
|
Added an argument ('extended' or 'ext') that outputs the four-base probs in a long format.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@485 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-21 22:27:26 +00:00 |
asivache
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521e202a10
|
updated interface
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@482 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-21 21:07:20 +00:00 |
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asivache
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55ca272919
|
reimplemented; now implements Genotype interface instead of AllelicVariant
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@481 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-21 21:06:42 +00:00 |
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hanna
|
eafb4633ba
|
Temporary workaround for samtools index bug: there seems to be an off-by-one error. Will file bug report.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@470 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-17 23:14:41 +00:00 |
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asivache
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f2f9fa3ed4
|
doc added
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@464 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-17 16:43:25 +00:00 |
|
hanna
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d639ec3776
|
Remove some copied code to make sure the traversal engine stays in sync with the locus context provider.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@463 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-17 16:41:56 +00:00 |
depristo
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50ae1763f7
|
Support for -continue_after_errors flag in the validating pileup walker in case you want to see errors as they arise, rather than aborting greedily
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@461 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-17 03:13:11 +00:00 |
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depristo
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ee5ab9536f
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trivial checking / flagging issues to enable testing of merging iterator performance
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@460 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-17 03:11:59 +00:00 |
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depristo
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dbf2344cef
|
Fixes for including duplicate reads in the locus traversal; now checks that the ref arg is provided when needed
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@459 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-17 01:27:36 +00:00 |
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hanna
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01be8f09e3
|
Exception cleanup. All our non-runtime exceptions should extend from StingException, StingException needs to be lower in the tree to build.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@457 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-16 22:17:25 +00:00 |
|
aaron
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e5c80e59dc
|
fixed the case when you're not seeking, it didn't initalize
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@456 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-16 22:16:03 +00:00 |
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hanna
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165e504d1c
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Turn on new TraverseLociByReference is now only dependent on the -et flag. REGION_STR does not matter.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@454 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-16 19:45:47 +00:00 |
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aaron
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12e1f192c4
|
Fixed a bug in this code where it would eat reads that didn't start at the beginning of the provided interval. This should fix / help fix Kristian problem
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@453 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-16 18:42:00 +00:00 |
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asivache
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835f1067d8
|
added isHom() and isHet() queries to the Genotype interface (with the obvious meaning)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@452 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-16 18:41:39 +00:00 |
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kcibul
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d35a542bb9
|
* fixed bug where the merged header was not being set on the read (although the read group was)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@445 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-16 12:53:07 +00:00 |
|
asivache
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0d324354ae
|
separate interface for genotypes as opposed to (population) allelic variants
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@443 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-16 03:55:16 +00:00 |
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depristo
|
7261787b71
|
Fixed potential bug with next() operation returning empty contexts when a read contains a large deletion. We can now use the look ahead safely...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@438 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-15 21:38:28 +00:00 |
|
aaron
|
e70aecf518
|
bug fix, but important
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@437 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-15 21:07:20 +00:00 |
|
aaron
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67ea66c866
|
Bug fix
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@434 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-15 19:12:18 +00:00 |
|
depristo
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1edfe48194
|
Better debugging output with .debug
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@433 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-15 19:09:18 +00:00 |
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depristo
|
9cc808104e
|
Fixed subtle bug in permitting EXPAND_WINDOW to be > 1. We now use the right window size so we avoid including empty hangers. There's still a rare bug to sort out, which occurs in the case where a read with an indel can generate empty hangers.
Also cleaned up the debugging output.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@432 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-15 19:08:26 +00:00 |
|
aaron
|
180ff13290
|
Added a bunch of changes to support the new MicroManager code
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@431 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-15 18:29:38 +00:00 |
|
aaron
|
12407b5b1a
|
Deleted the old file
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@427 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-15 13:55:01 +00:00 |
|
aaron
|
6db9127f90
|
Added changes to shattering, refactored SAMBAM into SAM
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@426 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-15 13:52:56 +00:00 |
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depristo
|
24722a442e
|
Slight code cleanup
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@421 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-14 22:21:36 +00:00 |
|
aaron
|
13b0995d54
|
Adding an iterator that bounds the number of reads
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@419 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-14 22:18:31 +00:00 |
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depristo
|
72a3d84ed2
|
General purpose pileup code -- you can use these features to obtain detailed pileup data from reads and offsets. Useful for all pileup based walkers. Expanded support for rodSAMPileup to enable the new ValidatingPileupWalker, which takes a samtools pileup output and checks that GATK gives identical output as samtools on a per base and per qual pileup. It's going to be a very useful validation tool.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@418 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-14 22:13:10 +00:00 |
|
hanna
|
0629f79049
|
Moved fasta support files into their own package.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@408 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-14 18:13:23 +00:00 |
|
aaron
|
eb4b4a053b
|
A bunch of updates to the SAM/BAM data source, along with test cases for the merging of multiple files (it works!).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@399 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-14 14:19:20 +00:00 |
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kiran
|
30121534ed
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Outputs the secondary bases and quals (if available) in verbose mode. Prefixed with the tag 'SQ='.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@398 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-14 13:58:28 +00:00 |
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depristo
|
8b2c2e677b
|
Uses the cleaner new GenomeLoc(read) syntax
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@396 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-14 00:55:43 +00:00 |
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depristo
|
1cee7948ab
|
Added lots of assertions to check for problems.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@395 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-14 00:55:19 +00:00 |
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depristo
|
794360c410
|
Added verbose option to show mapping qualities and base qualities as ints!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@394 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-14 00:54:48 +00:00 |
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depristo
|
cc75e8f712
|
Uses the cleaner new GenomeLoc(read) syntax
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@393 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-14 00:53:58 +00:00 |
|
asivache
|
8e6093d5a5
|
remove mom/dad/kid cmd line arguments that were needed for mendelian walker; now we can use generic track binding!!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@389 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-14 00:45:34 +00:00 |
|
aaron
|
887adcfc7f
|
Some minor fixes to the last check-in
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@387 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-13 18:24:51 +00:00 |
|
aaron
|
f2d0d73309
|
removed old shard strategy code
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@386 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-13 18:13:45 +00:00 |
|
aaron
|
dd604799dc
|
Added some new code for shard support over reads
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@385 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-13 18:11:43 +00:00 |
|
hanna
|
e91a429c58
|
A class to print out as much context about the given locus site as is possible. Useful for testing traversal engines -- run old and new code across a given region and diff the output to make sure they have the same context.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@383 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-13 15:29:55 +00:00 |
|
asivache
|
b4136b6d6e
|
a few tweaks to make it more robust: ignore reads with cigars containing anything but I,D,M; don't set up contig ordering manually, rely upon reference sequence and its dictionary; don't die if a record does not have NM tag, but faal back to direct counting instead; now requires reference as a cmdline arg
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@378 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-13 04:49:19 +00:00 |
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kiran
|
756e6c61d8
|
Strictness args are presented as lowercase in the help, but only accepted if uppercase. Changed help to list the valid arguments in uppercase.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@376 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-13 00:50:19 +00:00 |
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kcibul
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c7777d46d6
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* re-enabled setting of sequence dictionary information on GenomeLoc
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@366 348d0f76-0448-11de-a6fe-93d51630548a
|
2009-04-12 02:44:14 +00:00 |