bfbca8b194
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-12 12:11:58 -04:00
d7d15019dd
Adding support for other simple header line types (e.g. ALT) and cleaning up the interface a bit.
2011-07-12 01:16:21 -04:00
400b0d4422
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-11 23:38:57 -04:00
d5056ad899
Merge branch 'master' into diffit
2011-07-11 23:16:15 -04:00
893cc2e103
Making the package public, so there's no dependances from public -> private
2011-07-11 23:15:08 -04:00
5e593793af
DiffEngine utility function simpleDiffFiles
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printSummaryReport now uses GATKReport for nice formating
Moved print formatting arguments into inner class provided to printing functions themselves, not the class
BAMDiffableReader only reads 1000 entries to avoid performance issue. Work around for BAM files with non-unique names
Uncommented all of the incorrectly commented out CombineVariants integrationtests
BaseTest now uses DiffEngine to provide inline differences to VCF and BAM files
2011-07-11 23:10:27 -04:00
d11155ce2e
Merge branch 'master' of ssh://gsa3.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-11 19:19:54 -04:00
e93052a51e
When generating the QGraph, don't regenerate if there aren't scatter/gather jobs.
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Fixed a display issue with the number of milliseconds that Queue has tried to contact LSF.
2011-07-11 19:17:58 -04:00
e3748675db
Support for VCF 4.1 header counts
2011-07-11 17:40:45 -04:00
f54c2ae3b4
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-11 16:26:27 -04:00
d6517adb42
Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-11 16:16:37 -04:00
86890c6357
N and K (in binomial probability) got switched in RFA Walker with the last commit. No longer will NaNs be produced.
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Added: TableToVCF. Kind of a longer-term project, but there are lots of variant calls available in a weird tabular format. I used this to convert Ju Et Al small indels to VCF. I'll check against the 1000G ASN superpopulation calls to see if we see a good amount of recapitulation, and if so, i'll put them in unvalidated comparisons. Minor chances to the TableCodec and TableFeatures to allow for this (the codec can sometimes drop a column, and the feature now allows you to grab on to its header).
2011-07-11 16:16:15 -04:00
b327fa3779
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-11 15:20:45 -04:00
41db509a17
A simple python program for downloading S3 logs in the cron script.
2011-07-11 15:20:01 -04:00
d587856f2d
Private feature to input a list of family descriptions from a file and to look for MV's on all of these. Feature can also output a detailed description of the violation into a separate file
2011-07-11 14:17:59 -04:00
a18380ab96
Merged bug fix from Stable into Unstable
2011-07-11 12:16:50 -04:00
8a78414432
Removed TileCovariate as a dependency for AnalyzeCovariates.jar
2011-07-11 12:10:11 -04:00
6e7b5e1e7a
Merged bug fix from Stable into Unstable
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Merge branch 'master' into unstable
2011-07-08 21:19:45 -04:00
7fbc5987d0
Merge branch 'master' of ssh://delangel@nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-07-08 21:17:32 -04:00
68e19edf59
Merged bug fix from Stable into Unstable, and resolved merge conflicts.
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Conflicts:
build.xml
settings/ivysettings.xml
2011-07-08 15:50:31 -04:00
a3c9d9c3ff
Fixing Contracts for Java, and enabling contracts by default for unit/integration tests.
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The NullPointerException we were seeing when trying to run with contracts enabled was being caused
by an outdated version of the asm library.
To run tests without contracts and disable their compilation, pass in "-Duse.contracts=false" to ant.
Also did some minor unrelated cleanup in build.xml
2011-07-08 15:34:39 -04:00
bd29236684
Merge branch 'master' into diffengine
2011-07-08 14:08:17 -04:00
8de82f3974
Updated names to be more reflective of the fact that this works for exomes and WG now.
2011-07-08 14:07:28 -04:00
ae02eabc93
Since it now works with all classes of variants, should really be renamed
2011-07-08 14:04:59 -04:00
2ea36b06cc
Really works now with files where (1) there's no functional annotation and (2) there's no indel calls.
2011-07-08 14:04:00 -04:00
38d9b9b568
A printf from debugging made it in in some prior commit.
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The read transform adding the AI tag can cause an exception for widowed reads -- added a check for this case, preventing blowup.
2011-07-08 13:13:58 -04:00
51338cbe07
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-08 12:49:00 -04:00
224574424e
Bug fix: if we're genotyping a very long indel (>100 bp) fail gracefully instead of with an array out of bounds exception
2011-07-08 12:48:49 -04:00
2a4b3ae4a2
Cleaning up / removing most of the monkeying around with annotation values that happens in VariantDataManager
2011-07-08 12:48:33 -04:00
f7d188232f
Merge branch 'master' of ssh://tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-08 12:32:32 -04:00
f7b7467139
Moving the private filter package from sting/filters to sting/gatk/filters, updating package name and imports. This was preventing walkers from running. (Thanks, Matt!)
2011-07-08 12:28:46 -04:00
8add2a3866
Merge branch 'master' into diffengine
2011-07-08 09:15:54 -04:00
9a14b914b7
Not sure why this happened...
2011-07-07 23:09:12 -04:00
5ed7243b64
Removing old oneoffs walkers as I threatened
2011-07-07 23:02:41 -04:00
cc143493e3
Merged bug fix from Stable into Unstable
2011-07-07 23:01:24 -04:00
4cfe0dd857
Test for bad alleles so that we don't generate IndexOutOfBoundsExceptions
2011-07-07 23:01:03 -04:00
b9ffe592c4
Now supports files without indels calls in them
2011-07-07 22:32:47 -04:00
609ca0baab
canRead() now implemented by looking for BAM_MAGIC value BAM\1 in file, and for the ##fileformat=VCFv4 header line in the VCF file. BAM reader now fully operational, and with a unit test. All unit tests work now. Minus function / class documentation the system is pretty stable and usable.
2011-07-07 22:02:45 -04:00
3d4f0e9dd7
Now supports the case where you have multiple AC values in the info field.
2011-07-07 17:21:15 -04:00
adb6fc910e
Merged bug fix from Stable into Unstable
2011-07-07 16:24:57 -04:00
ce5a1c2cbe
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-07-07 16:21:27 -04:00
1a42a5b4ec
Refactored oneoffs to properly be in the private package
2011-07-07 16:16:12 -04:00
58c841ce1b
Merged bug fix from Stable into Unstable
2011-07-07 16:15:57 -04:00
13519c2c3d
Moved PhaseByTransmission per Eric's request
2011-07-07 16:14:14 -04:00
231e4bdb11
Merged bug fix from Stable into Unstable
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Merge branch 'master' into unstable
2011-07-07 15:41:01 -04:00
06f12eca56
Move from qscript/delangel to qscripts/calling
2011-07-07 15:39:48 -04:00
d344317f8b
Merged bug fix from Stable into Unstable
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Merge branch 'master' into unstable
2011-07-07 15:27:35 -04:00
8a571e3488
Move IndelCountCovariates package to gatk.walkers
2011-07-07 15:25:37 -04:00
212e9a1a0c
Fixing unstable build after stable commit
2011-07-07 15:18:57 -04:00
11d9a0473a
Merged bug fix from Stable into Unstable
2011-07-07 15:03:58 -04:00
Guillermo del Angel
Eric Banks
Mark DePristo
Khalid Shakir
Christopher Hartl
David Roazen
Ryan Poplin
Menachem Fromer
Kiran V Garimella