f26ffeaea0
bug fixes
2011-07-04 20:48:45 -04:00
04df153f47
bug fixes
2011-07-04 20:45:10 -04:00
7a04872a3f
bug fixes
2011-07-04 20:33:59 -04:00
08bc843d4c
SelectVariants can get a table to boost AF when choosing randomly
2011-07-04 20:23:22 -04:00
e634ef0599
Merge branch 'master' of ssh://delangel@nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-04 19:43:35 -04:00
983670e6ac
Merge branch 'master' of ssh://gsa1.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-03 15:57:34 -04:00
fac082de64
Report only highest AF and AC in multiallelic records in VariantsToTable or else R can't parse table
2011-07-03 14:32:12 -04:00
abe9480c6d
Merge branch 'master' of ssh://delangel@nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-02 21:19:15 -04:00
06a1ab1820
Merge branch 'master' of ssh://gsa1.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-02 18:42:27 -04:00
fb315b5f8c
Merge branch 'incoming'
2011-07-02 18:10:48 -04:00
41d46059e7
fixing bad format statement
2011-07-02 18:09:17 -04:00
3804afeb8a
Merge branch 'incoming'
2011-07-02 17:55:39 -04:00
781c0c33a4
Use the worst X% of calls in addition to the bad training sites list. Don't include the already added calls in the calculation of X%
2011-07-02 17:55:10 -04:00
4f821c081b
Merged bug fix from Stable into Unstable
2011-07-02 17:42:45 -04:00
14eb7873a0
Reorganizing private oneoff qscripts
2011-07-02 17:41:19 -04:00
6b8af6afd8
Merge branch 'master' of ssh://gsa1.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-02 17:15:56 -04:00
fdc2ebb321
Adding ability to specify in VQSR a list of bad sites to use when training the negative model. Just add bad=true to the list of rod tags for your bad sites track.
2011-07-02 17:15:13 -04:00
09af6bbc6c
Ugh - backed out experimental code not for public consumption unintendedly committed
2011-07-02 16:58:57 -04:00
c6c0dba040
Merge branch 'master' of ssh://delangel@nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-02 16:45:34 -04:00
b66581dc45
More changes on consensus script
2011-07-02 16:45:08 -04:00
4532a84314
Merged bug fix from Stable into Unstable
2011-07-02 10:48:55 -04:00
14375c3ba9
Moving my very first walkers into the archive.
2011-07-02 10:45:12 -04:00
5faf40b79d
Moving AnalyzeAnnotations into the archive because it has outlived its usefulness.
2011-07-02 10:39:53 -04:00
43959e6780
Moving old R scripts into the archive
2011-07-02 10:33:27 -04:00
17ff5bb094
Variant records coming out of the VQSR are now annotated with which input annotation was most divergent from the Gaussian mixture model. This gives a general sense for why each variant was removed from the callset.
2011-07-02 09:55:35 -04:00
635dc5de4b
New hyper-parallel structure for indel consensus: each 3 MB chunk is divided into 100 subchunks so I can fit in hour queue. Got rid on indel realignment and snp parts, use BTI to compute only at input sites.
2011-07-01 20:51:01 -04:00
c65e52f88a
Merged bug fix from Stable into Unstable
2011-07-01 20:50:56 -04:00
b6bc64a0c8
Cleanup of the utils.broad package.
...
Using Picard IoUtils on sample names.
2011-07-01 20:47:03 -04:00
0c9105ca22
Minor fix of description
2011-07-01 18:07:35 -04:00
358cf98b67
Merged bug fix from Stable into Unstable
2011-07-01 17:27:07 -04:00
444eae316c
Moving these supported perl scripts to public
2011-07-01 17:26:25 -04:00
95abb2e14a
Merged bug fix from Stable into Unstable
2011-07-01 17:12:21 -04:00
cfdece6dd8
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-07-01 17:11:32 -04:00
1c1cd373d8
Fix to make liftOver.pl work with new file structure
2011-07-01 17:07:22 -04:00
a025f85c08
Merged bug fix from Stable into Unstable
2011-07-01 16:44:33 -04:00
546e7777fa
Re-fixing paths in pipeline tests after example qscripts got moved.
2011-07-01 16:39:10 -04:00
b19e22aed9
Merged bug fix from Stable into Unstable
2011-07-01 16:20:25 -04:00
e9030a7bfd
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-07-01 16:19:35 -04:00
d631f645c4
Merged bug fix from Stable into Unstable
2011-07-01 16:16:31 -04:00
b0fb63e20a
moving the example scala scripts to the qscripts package.
2011-07-01 16:14:59 -04:00
04971aecc9
Merged bug fix from Stable into Unstable
2011-07-01 16:04:50 -04:00
d647ea4fdc
Long-delayed change to CachingIndexedFastaSequenceFile. Made the cache
...
non-static to avoid problems when multiple references are used within the same
thread (eg., during integration tests). This should kill the intermittent
IndelRealignerIntegrationTest failures.
2011-07-01 16:04:30 -04:00
d19351f71a
Added capability of running multiple bam files in the same directory.
2011-07-01 16:02:28 -04:00
350a76d5dd
Merged bug fix from Stable into Unstable
2011-07-01 13:53:46 -04:00
11d4af0e75
Path-related fixes to the private queue pipeline tests.
2011-07-01 13:41:34 -04:00
9644f104c4
Fixes to the queue pipeline tests to account for the new directory structure.
2011-07-01 13:13:24 -04:00
7159b14e76
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-01 10:53:49 -04:00
bf29ca21cd
Some bugfixes for yesterday's sparse data population enhancements.
2011-07-01 10:53:07 -04:00
bf3cd1ee72
Merged bug fix from Stable into Unstable
2011-06-30 18:30:22 -04:00
4b17f34640
Fixes to the packaging system to work with the new directory structure.
...
Also added a few R scripts to the list of files to include in the resources
directory of the binary distribution, at Ryan's request.
2011-06-30 18:27:17 -04:00
Guillermo del Angel
Mark A. DePristo
Ryan Poplin
Khalid Shakir
Eric Banks
David Roazen
Mauricio Carneiro
Matt Hanna