9111966261
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
2012-11-20 12:19:58 -05:00
e0e8b51906
Merge branch 'master' of gsa2:/humgen/gsa-scr1/chartl/dev/unstable
2012-11-20 11:33:40 -05:00
5a97d03709
fix output names
2012-11-20 11:27:53 -05:00
553e635415
Bring miscellaneous additional infrastructure scripts under version control
2012-11-19 16:12:05 -05:00
d07f3d4a5a
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
2012-11-19 11:17:02 -05:00
3b78f3d982
fix hs metrics file name
2012-11-19 10:38:10 -05:00
4f243acaa6
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
2012-11-19 10:34:44 -05:00
28b8401867
Checking in new git setup script
2012-11-19 10:02:18 -05:00
d46ffab0f2
added file1 and file2 parameters back for backwards compatibility
2012-11-19 09:58:51 -05:00
f0b8a0228f
Quick fix for HC refactoring: when copying over Haplotype objects, make sure to copy over the artificial allele used to create it too.
2012-11-19 09:57:55 -05:00
e68dc24aae
Git infrastructure updates
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-Webhook handler
-Infer From: address from last commit in push rather than from userid
running the git process
2012-11-19 09:45:54 -05:00
e1a5c3ce7a
Revert "Second test of new repos. Please ignore."
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This reverts commit 077532d870ddf53ec514b98f14534ca7dbf55331.
2012-11-19 09:34:32 -05:00
9fc63efc30
Second test of new repos. Please ignore.
2012-11-19 09:34:15 -05:00
ff180a8e02
Significant refactoring of the Haplotype Caller to handle problems with GGA. The main fix is that we now maintain a mapping from 'original' allele to 'Smith-Waterman-based' allele so that we no longer need to do a (buggy) matching throughout the calling process.
2012-11-19 09:09:57 -05:00
78ce822b6f
Protect against NPE when using non-GATK reports for inputs expecting valid GATK reports
2012-11-19 09:07:04 -05:00
2a16d6fa55
Revert "Testing out the new github-hosted repos. Please ignore."
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This reverts commit b6bf66cd088754e7fd3d5f105ca8b2551237f183.
2012-11-19 08:07:19 -05:00
855a68ae39
Testing out the new github-hosted repos. Please ignore.
2012-11-19 08:06:58 -05:00
918d83b5de
added TrivialTask Q script
2012-11-15 14:14:19 -05:00
b70fd4a242
Initial testing of the Active Region Traversal contract
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- TODO: many more tests and test cases
2012-11-15 10:08:00 -05:00
a68e6810c9
Back off experimental code that escaped last commit, not for general use yet
2012-11-14 14:45:15 -05:00
89bbe73a43
Commenting out CMI pipeline test that wasn't meant to be in GATK repository (why was this merged??)
2012-11-14 14:39:04 -05:00
3771d074dc
Merge branch 'master' of ssh://gsa3/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-11-14 14:37:43 -05:00
8b749673bc
centralize header element removal in reduce reads
2012-11-14 13:59:34 -05:00
843384e435
Rename hg19 files in bundle to b37 since that's what they are
2012-11-14 11:47:09 -05:00
e35fd1c717
Merging CMI-0.5.0 and GATK-2.2 together.
2012-11-14 10:42:03 -05:00
a079d8d0d1
Breaking the utility to write @PG tags for SAMFileWriters and StingSAMFileWriters
2012-11-14 10:33:22 -05:00
dba31018f4
Implementation of BySampleSAMFileWriter
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ReduceReads now works with the n-way-out capability, splitting by sample.
DEV-27 #resolve #time 3m
2012-11-14 10:33:22 -05:00
8503db6e87
moving cancer pipeline qscript over to cmi-cancer
2012-11-14 10:33:21 -05:00
de53c32361
moving to cmi-cancer
2012-11-14 10:33:21 -05:00
ff63c53961
Increase bwa mem limit by 1 Gb - see if we can avoid random job failures that way
2012-11-14 10:33:21 -05:00
a17cd54b68
Co-Reduction implementation in ReduceReads
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ReduceReads now co-reduces bams if they're passed in toghether with multiple -I. Co-reduction forces every variant region in one sample to be a variant region in all samples.
Also:
* Added integrationtest for co-reduction
* Fixed bug with new no-recalculation implementation of the marksites object where the last object wasn't being removed after finalizing a variant region (updated MD5's accordingly)
DEV-200 #resolve #time 8m
2012-11-14 10:33:21 -05:00
f4511c0d6f
made parameters not required, fixed some null file names
2012-11-14 10:33:21 -05:00
1bfe73397f
made parameters not required, switched date sequenced format, bug fixes in pulling remote files
2012-11-14 10:33:21 -05:00
f9cc68ce17
pull metadata from metadata service
2012-11-14 10:33:20 -05:00
6d59dd3455
Scala classes were only returning direct subclasses (confirmed when inspected in debugger) so changed PluginManager to allow specifying the explicit subclass.
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Removed some generics from PluginManager for now until able to figure out syntax for requesting explicit subclass.
QStatusMessenger uses a slightly more primitive Map[String, Seq[RemoteFile]] instead of Map[ArgumentSource, Seq[RemoteFile]].
Added an QCommandPlugin.initScript utility method for handling specialized script types.
2012-11-14 10:33:20 -05:00
42ddf51156
Merged bug fix from Stable into Unstable
2012-11-14 10:29:09 -05:00
49869344b8
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-11-14 09:42:35 -05:00
040a27d2d2
minor typo in SortROD; Few changes in the CatVariants (still under development)
2012-11-14 09:36:32 -05:00
cab8ba7c75
Breaking the utility to write @PG tags for SAMFileWriters and StingSAMFileWriters
2012-11-13 16:16:14 -05:00
ba41f65759
Protect against NPEs in SelectVariants by checking for missing Genotypes
2012-11-13 11:53:39 -05:00
c7335c9902
Having a malformed GATK report is a User Error
2012-11-13 11:53:12 -05:00
525cf331f4
Don't catch a User Error and re-throw as a Reviewed Exception. That makes Eric unhappy.
2012-11-13 11:52:47 -05:00
95a4ba57bf
Implementation of BySampleSAMFileWriter
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ReduceReads now works with the n-way-out capability, splitting by sample.
DEV-27 #resolve #time 3m
2012-11-13 02:09:58 -05:00
1f23a82aa4
moving cancer pipeline qscript over to cmi-cancer
2012-11-09 10:18:22 -05:00
d3f9465307
moving to cmi-cancer
2012-11-09 10:01:02 -05:00
e93d461910
Adding integration test to BQSR for the csv file
2012-11-09 09:11:04 -05:00
ee776e996a
Merged bug fix from Stable into Unstable
2012-11-09 08:35:51 -05:00
66cbaaee31
Fixed nasty bug in BQSR csv file creation:
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numbers larger than 999 in the Errors column were printed out with commas (which looks like a separate column).
This wasn't caught earlier because there are no integration tests covering the csv. I'll add one into unstable in a sec.
2012-11-09 08:33:55 -05:00
e9183d9fe0
Fix bugs as reported on the forum: BED needs to be explicitly set as the default output format and the output didn't actually adhere to the BED spec.
2012-11-08 15:07:47 -05:00
17ab3a39d5
Make the --intermediate_csv_file argument un-hidden.
2012-11-08 14:35:23 -05:00
Menachem Fromer
Chris Hartl
Douglas Voet
David Roazen
Ami Levy-Moonshine
Eric Banks
Scott Frazer
Joel Thibault
Guillermo del Angel
Mauricio Carneiro
Kristian Cibulskis
kshakir