30768eccbb
Big change to PSP2: Amplicon sequence no longer lower-cased for repetitiveness, but instead for non-uniqueness via alignment by bwa. Performance heavily dependent on length of sequence (duh), with size=30 a good balance, but default is 20 because that's the default length of a sequenom primer. Indentation changes to other stuff.
2011-07-12 18:33:12 -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
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by an outdated version of the asm library.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
50111db2b7
Fixing non-determinism in single-threaded VQSR by moving references to cern.Normal over to the static random generator available in GenomeAnalysisEngine
2011-07-07 15:02:48 -04:00
fe8e2c305c
Adding dev qscript which I used to perform the VQSR in exome by sample size experiment
2011-07-07 13:37:29 -04:00
0df31f3d78
Simple usability improvements to the DiffEngine and DiffObjectsWalker. Can specify min count for summarized diff objects for display.
2011-07-07 11:16:42 -04:00
ccf34f7e45
(1) Added very useful helper class TestDataProvider to BaseTest that making creating data providers for TestNG far easier
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(2) DiffEngine now officially working with with summaries. Extensive UnitTests all around!
2011-07-06 21:57:22 -04:00
52f6f9fdcc
Merged bug fix from Stable into Unstable
2011-07-06 16:05:48 -04:00
54121eb082
Catch malformed bams that cause the writer to run in infinite loops
2011-07-06 16:05:08 -04:00
3ed6d494ce
Huh, guess I forgot to commit this one.
2011-07-06 15:58:12 -04:00
ebf117f1fe
Change packages to reflect current structure. Remove @Overrides on interface methods.
2011-07-06 14:05:50 -04:00
76a01a7453
Merged bug fix from Stable into Unstable
2011-07-06 12:53:09 -04:00
14fee4ccbd
Patch from Bob to deal with symbolic alleles: these weren't getting padded but they should be.
2011-07-06 12:51:44 -04:00
Christopher Hartl
Mark DePristo
David Roazen
Guillermo del Angel
Ryan Poplin
Eric Banks
Menachem Fromer
Kiran V Garimella