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
28c7492b98
Increase bwa mem limit by 1 Gb - see if we can avoid random job failures that way
2012-11-07 06:45:59 -08:00
2da76db945
Updating integration tests
2012-11-06 22:23:05 -08:00
e6f33a2e34
Merge branch 'master' of ssh://gsa2/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-11-06 20:55:34 -08:00
f4d4846435
Merged bug fix from Stable into Unstable
2012-11-06 20:53:54 -08:00
15b8c08132
Apparently CIGAR elements can have 0 length according to the spec, but 0Ms were causing left alignment of indels to fail. Fixed.
2012-11-06 20:53:33 -08:00
0a2dded093
Fixes for bugs uncovered by unit tests
2012-11-06 16:07:40 -08:00
b07106b3a7
Reimplement the allele biased downsampling to be smarter. Now we don't blindly pull n% of reads off of each allele. Instead, we try all possible genotype conformations for the contaminating sample and choose the one that provides the best genotype for the target sample (based heuristically on allele balance). This method allows us to save some of the reads that belong to the target sample, which should make Daniel M happy. Added unit tests to test the biased downsampling functionality.
2012-11-06 14:39:58 -08:00
6f6106d50c
Merge branch 'develop' of https://github.com/broadinstitute/cmi-gatk into develop
2012-11-06 14:44:00 -05:00
9ecd73ec7d
made parameters not required, fixed some null file names
2012-11-06 14:43:15 -05:00
4a2ffd7c8d
made parameters not required, switched date sequenced format, bug fixes in pulling remote files
2012-11-06 14:00:36 -05:00
2c0bf89961
Co-Reduction implementation in ReduceReads
...
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
2012-11-06 13:49:07 -05:00
f78d8fa157
Merge branch 'master' of gsa2:/humgen/gsa-scr1/chartl/dev/unstable
2012-11-06 10:21:17 -05:00
48112c9337
pull metadata from metadata service
2012-11-05 22:45:46 -05:00
bff7803f3a
update the Mills_and_1000G_gold_standard file
2012-11-05 13:00:40 -05:00
Eric Banks
David Roazen
Scott Frazer
Joel Thibault
Guillermo del Angel
Mauricio Carneiro
Kristian Cibulskis
Douglas Voet
kshakir
Ami Levy Moonshine
Christopher Hartl