38740b0ff5
First working version of the DiffNode readers for VCF and BAM files. Unit tests confirm the readers are approximately working. Skeleton of a working DiffObjects walker that will be able to provide detailed information about how exactly two files of the same type differ, so long as the files are supported by the DiffNode structure.
2011-07-04 16:11:42 -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
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
91f8ab115d
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-06-30 18:15:53 -04:00
419bf259ee
Large number of bugfixes for bugs encountered while trying to scale up preQC database generation to all reprocessed data:
...
- Better support for missing data, esp. in eval files.
- More R-compatible date formatting.
- Some of the AlignmentSummaryMetrics were only for first of pair.
- Some of the InsertSizeMetrics retrieved data for only one pairing orientation.
- More/better command-line customization.
2011-06-30 18:03:59 -04:00
510efa3313
Merged bug fix from Stable into Unstable
2011-06-30 15:27:04 -04:00
5786b51bcf
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-06-30 15:26:28 -04:00
761347b8d5
The VariantContext utility method used by SelectVariants wasn't checking the filter status (unfiltered vs. passing filters) and always returned a VC that was passing filters. This is fixed and the md5 from the VCF Streaming test has been re-updated.
2011-06-30 15:26:09 -04:00
47b47078ad
Merged bug fix from Stable into Unstable
2011-06-30 15:22:14 -04:00
Mark A. DePristo
Ryan Poplin
Guillermo del Angel
Khalid Shakir
Eric Banks
David Roazen
Mauricio Carneiro
Matt Hanna