52f6f9fdcc
Merged bug fix from Stable into Unstable
2011-07-06 16:05:48 -04:00
54121eb082
Catch malformed bams that cause the writer to run in infinite loops
2011-07-06 16:05:08 -04:00
3ed6d494ce
Huh, guess I forgot to commit this one.
2011-07-06 15:58:12 -04:00
ebf117f1fe
Change packages to reflect current structure. Remove @Overrides on interface methods.
2011-07-06 14:05:50 -04:00
76a01a7453
Merged bug fix from Stable into Unstable
2011-07-06 12:53:09 -04:00
14fee4ccbd
Patch from Bob to deal with symbolic alleles: these weren't getting padded but they should be.
2011-07-06 12:51:44 -04:00
a5ad603b35
Gah. Missed one.
2011-07-06 12:15:41 -04:00
759bc25643
Get rid of the dumb backups
2011-07-06 12:15:04 -04:00
f5890b1715
Moving RFA from string/walkers to sting/gatk/walkers (PSP2 as well). Dumb emacs backups committed accidentally, will be removed shortly.
2011-07-06 12:12:25 -04:00
515553c801
Merged bug fix from Stable into Unstable
2011-07-06 11:34:13 -04:00
0b86958a56
Merge branch 'master' of ssh://gsa3/humgen/gsa-scr1/gsa-engineering/git/stable
2011-07-06 11:33:15 -04:00
c93d0b37a8
Fixed namespace of the pipeline classes.
2011-07-06 11:32:46 -04:00
bdef233d4d
Merged bug fix from Stable into Unstable
2011-07-06 10:05:02 -04:00
e8ed6b7f0f
Adding more comments to main VQSR walker. Fixing copyright lines. Bug fix for default paths to now point to public/R/ instead of R/ Bug fix in VQSR for the path to the R scripts not ending in a slash.
2011-07-06 10:01:14 -04:00
8e8b901d12
Merged bug fix from Stable into Unstable
...
Merge branch 'master' into unstable
2011-07-06 09:57:55 -04:00
81a4d18468
Mark several indel-related arguments as @Hidden
2011-07-06 09:56:38 -04:00
7b699f8b17
Switched GridEngine from looking from environment variable to using embedded jar.
2011-07-05 21:59:00 -04:00
407a0e535f
Merged bug fix from Stable into Unstable
2011-07-05 16:34:21 -04:00
5298e3a942
Making the outputDir optional. Default = ./
2011-07-05 16:30:41 -04:00
7d3dfdfdf2
Updating the MDCP to use the classpath for the GATK jar, removing -gatk parameter.
2011-07-05 16:30:10 -04:00
a765c08381
New home for the ReducedBAMEvaluation qscript.
2011-07-05 13:58:50 -04:00
592e79a4ba
There is no pretty way to do this unfortunately.
...
How to remove files from STABLE, sync with UNSTABLE but maintain the files there :
1. Remove all files from STABLE commit then push.
2. Do the 'bug-fix' routine to update UNSTABLE. <-- here you will also remove the files from unstable.
3. Go to unstable and revert the commit where you deleted the files.
This way you keep them in Unstable, remove from stable and safely maintain the repositories going their separate ways.
ps: this is what I did here :-)
This reverts commit 4dbd5e476cbe441c2a9fa67e88c3b4dbf57b3b9e.
2011-07-05 13:32:21 -04:00
90f8de37d5
Merged bug fix from Stable into Unstable
2011-07-05 13:26:41 -04:00
cd53e5a131
Removing the ReduceReads files and package from the stable repo. It should only exist in private/unstable.
2011-07-05 13:22:55 -04:00
d787f43df7
Merged bug fix from Stable into Unstable
2011-07-05 01:04:28 -04:00
b38529309c
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-07-05 01:03:36 -04:00
e7e7cc390f
fixing a wrong refactor
2011-07-05 01:02:54 -04:00
8f5773fc5c
preparing the classes for future functionalities
2011-07-05 00:19:38 -04:00
514b9c1751
UnifiedGenotyper already has @input/@output annotations
2011-07-04 19:23:05 -04:00
3206c581ce
Cleaning up the gatk jar argument, as queue now uses the queue's classpath.
2011-07-04 19:10:54 -04:00
980580287a
Fixing with the new variantcontext location
2011-07-04 19:06:06 -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
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
Eric Banks
Christopher Hartl
Khalid Shakir
Ryan Poplin
Guillermo del Angel
Mauricio Carneiro
Mark A. DePristo