c8be7c3102
Keep SNPs and indels separately for batch merging; Add options to DepthOfCoverage to count fragments (to not double-count overlapping reads of same fragment); DepthOfCoverage should now support ReducedReads; Replace recusrion with loop in DoC/package.scala (for lists longer than 5000 elements)
2012-11-21 15:56:53 -05:00
8376c28728
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
2012-11-20 12:35:39 -05:00
d2a6e2526d
Fixed Input vs. Argument
2012-11-20 12:34:47 -05:00
9111966261
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
2012-11-20 12:19:58 -05:00
553e635415
Bring miscellaneous additional infrastructure scripts under version control
2012-11-19 16:12:05 -05:00
28b8401867
Checking in new git setup script
2012-11-19 10:02:18 -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
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
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
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
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
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
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
bff7803f3a
update the Mills_and_1000G_gold_standard file
2012-11-05 13:00:40 -05:00
659ec4b6b7
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-11-05 11:43:57 -05:00
fca6321be2
update the dbSNP file
2012-11-05 11:43:36 -05:00
bf7c832d25
Merged bug fix from Stable into Unstable
2012-11-02 19:23:11 -04:00
eae2d019cf
Refuse to package the GATK from a non-clean working directory
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Packaging from a non-clean working directory can result in an incorrect
jar. Now that we have external collaborators packaging and distributing
the GATK, not enforcing the clean requirement has become far too dangerous.
At the same time, invoking "clean" automatically through a direct
dependency would also be dangerous -- instead, it's better to error out
if a packaging target is invoked from a non-clean working dir.
2012-11-02 19:11:24 -04:00
0ab4022f23
Final r119 tribble jar
2012-11-02 14:30:33 -04:00
73157ae3d3
Allow each pipeline test the max of 10 hours to run
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The runtime of these tests is extremely variable -- sometimes they will complete almost instantly,
other times they will wait in an LSF queue for 5-10+ hours. Minimize timeout errors by setting the
timeout for these tests to the maximum of 10 hours.
2012-11-02 12:40:56 -04:00
f8a0a947e3
Critical bugfix for GSA-652 / Multi-threaded VCF -> BCF writing produces invalid intermediate file that fails on merging
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-- New tribble library now uses 64 bit sizes. The 26K VCF has so much data that low-level tribble block indices where overflowing their int size values. This includes a to-be-committed tribble jar that fixes this problem
-- See https://jira.broadinstitute.org/browse/GSA-652
-- Minor cleanup of error messages that were useful on the way to solving this monster problem
2012-11-02 09:09:59 -04:00
Menachem Fromer
David Roazen
Joel Thibault
Guillermo del Angel
Eric Banks
Mauricio Carneiro
Kristian Cibulskis
Douglas Voet
Scott Frazer
kshakir
Ami Levy Moonshine
Mark DePristo