zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
4,659 Commits
1 Branch
0 Tags
257 MiB
Commit Graph

3845 Commits (90711d445c9836dcd8b8a6d5a74aa45cfe66a0ae)

Author SHA1 Message Date
depristo 00491fcd2e Only see not writing GATK Run Report if you are running with debug enabled 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4437 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-06 14:09:21 +00:00
rpoplin 69485d6a7a Added command line argument for the max value of the allele count prior in VariantRecalibrator (--max_ac_prior). Default value increased to 0.99 from 0.95. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4436 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-06 14:00:53 +00:00
ebanks 3d564f4a29 reverting an accidental change from the dindel merge 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4434 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-06 03:08:09 +00:00
ebanks b5e148140b Officially fixed the UG priors; updated the default min MQ/BQs to pipeline values of q20 and min calling threshold to Q50 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4431 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-05 18:35:36 +00:00
fromer c6668bd49c Fixed bug in phasing, where mapping probability was incorrectly raised to the power of number of non-null bases [instead, it is just multiplied into phasing probability once] 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4430 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-05 17:07:31 +00:00
hanna 250c18e679 Error message fixes for the following issues: 
nvjpM4yOwQAu3fNGxi4oXLuVpKn6aAlf,1GL0OuXK2xKQfvbu34tWYgbojSVSLo0l,
ehEGBJOfgc4V7qj8W0Homf5ICuVK5Sm3,cZsreLm1CbY3aYKZhV7DOSvQNwur41zp,
GlrlyGEyP9kJDIRCQNFQp7BGJBXSzdDJ,hyz1uiHXr39ANmdZu9K1epOSX8EL3mDw,
q0n4EucZESCI4LZhQik306zD4VAuH2cb.  

Messages:
camrhG5tHzlY9WUSEVpVZGkU1tyJqKb5,s0OX2g7nYRctJxyFoQCa6clac9IsjHyi,
THIAtjllvYNlnTmiMnJEIHd2Ju4gqQIO,jwVk3JYZJNHloW7HO4LeGxFexknqro0v,
BFNRGOGmGGJNNPZqgeF1ikTNFfskbyLc,...

Were fixed in 4392.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4428 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-05 03:37:13 +00:00
ebanks aa00801108 remove reference to -mrl 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4423 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-04 17:27:01 +00:00
chartl f978c25b9d Perhaps both, Eric. Perhaps both. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4422 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-04 13:56:04 +00:00
chartl 0eb777612a Swap "." over to VCFConstants.MISSING_DEPTH_v3 
Why v3, you ask? Why not? Simply because v2 was a String so old and clunky, the sun would fizzle out and grow cold before any VCF could be successfully parsed.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4421 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-04 13:41:41 +00:00
chartl 74087c44ae Fixed a bug which caused a parsing exception when there was a variant with a dp field of ".", e.g. "GT:DP 0/1:." -- which can happen when using imputation. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4420 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-04 12:37:36 +00:00
ebanks 6448753cf7 Removed the SequenomValidationConvertor and renamed it VariantValidationAssessor since it no longer handles ped/sequenom files (but instead works on vcfs/variantcontexts). Updated all of the wiki docs, including adding instructions on how to convert ped files to vcf, a la Shaun Purcell. We now officially no longer support ped files everyone. Other misc cleanup in the code. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4419 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-04 02:11:38 +00:00
ebanks d8db48204e Fix typo and tell people not to post user errors 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4415 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-03 18:58:03 +00:00
ebanks 490e5e1b0f Better error when bad ref bases are provided 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4414 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-03 05:40:37 +00:00
aaron 64b7b3f83b fix for a recent change to the indexing code where we ignore the results of locking the file (this is bad), and as a result don't write the index; this should fix the build. 
Off to Yosemite in 4 hours, enjoy the week gsa folks!



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4410 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-02 04:35:11 +00:00
depristo 7551ba8249 Trival refactoring in preparation for on-the-fly indexing 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4409 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-01 22:32:59 +00:00
rpoplin 2f7892601c Useful debugging argument added to VariantRecalibrator to only use sites whose qual field is above --qual 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4406 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-01 21:08:55 +00:00
hanna 575c38fc04 Accidental fail to commit missing file. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4405 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-01 20:26:51 +00:00
delangel d4398f2686 silly bug fix: if I'm to do a short term hack to avoid -infinity likelihoods I might as well do it right. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4403 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-01 18:39:45 +00:00
hanna 8d25a5f9f2 A mechanism for supplying attribution text -- mainly useful for external 
walkers.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4402 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-01 18:31:19 +00:00
delangel e920badcc4 Temporary fix for case where genotype likelihoods are exactly (1,0,0) or (0,1,0) etc. at a site with new indel genotyper: this would make us blow up when converting to log space and try to assign genotypes at a site. A more robust solution is in the works. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4401 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-01 17:43:43 +00:00
rpoplin b83fdf8a17 Bug fix in AnalyzeAnnotations. Be sure the site is a biallelic, unfiltered SNP. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4400 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-01 13:09:46 +00:00
delangel fa9c21c020 More fixes for exact AF calculation model in new unified genotyper: 
a) Fixed bugs in new dynamic programming-based genotyper
b) Fixed up temp hack that handles extended pileups for now.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4398 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-01 02:32:50 +00:00
delangel eb67aee732 bug fix: forgot to uncomment code to compute genotype likelihoods 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4397 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-30 21:38:22 +00:00
delangel ece694d0af Next iteration on new UG framework: 
- Brought over exact AF estimation from branch (which is now dead). Exact model is default in UnifiedGenotyperV2.
- Implemented completely new genotyping algorithm given best AF estimate using dynamic programming, which in theory should be better than both greedy search and any HWE-based genotyper.
- Integrated and added new Dindel likelihood estimation model.
- Corrected annotators that would call readBasePileup: since we can be annotating extended events, best way is to interrogate context for kind of pileup and either readBasePileup or readExtendedEventPileup.

All changes above except last one are still in playground since they require more testing.




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4396 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-30 21:33:59 +00:00
hanna 4ea73bcfb1 Basic unit tests for WalkerManager. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4394 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-30 19:27:41 +00:00
hanna bf7fd08810 Fix newly-introduced bug in the PluginManager/DynamicClassResolutionException 
where, when the system can't find a plugin of the correct name, the system
prefers to crap all over itself and throw an unintelligible NullPointerException
rather than displaying an intelligent error.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4393 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-30 19:07:05 +00:00
hanna 14e19f4605 (Slightly) better exception text when SAM/BAM output file can't be created. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4392 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-30 18:43:22 +00:00
hanna 1fb8c86f6d Looks like we've got two competing models for an empty interval list: null and 
the empty list.  Score another victory for the integration tests.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4391 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-30 17:11:47 +00:00
hanna 78343be52c At some time in the recent past, we lost our ability to process the '-L all' 
argument.  Brought it back, and added an integrationtest to make sure it
stays around.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4390 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-30 15:58:43 +00:00
delangel e80742e72f Use -o as argument for output file in ProduceBeagleInputWalker, to be consistent with other walkers (you're welcome, chartl :)). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4386 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-29 22:46:39 +00:00
hanna 732aa32758 Every Sting app from now on will be forced into the US English locale. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4385 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-29 21:55:21 +00:00
fromer 20ffe484bc Added detection and INFO field marking of phasing inconsistencies (and optional filtration using --filterInconsistentSites) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4384 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-29 19:28:56 +00:00
rpoplin a6c7de95c8 By using the AC info field instead of parsing the genotypes we cut 78% off the runtime of VariantRecalibrator. There is a new argument to force the parsing of genotypes if necessary. Various other optimizations throughout. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4383 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-29 18:56:50 +00:00
ebanks 2d1265771f Fix for G: make sure to generate the genotype conformations in the grid for the target frequency when not using grid search for anything except the conformations 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4382 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-29 16:44:53 +00:00
delangel 4556e3b273 First iteration in filling up exact AF calculation with new refactored UG. Code computes EM iterations of exact AF spectrum and returns to caller. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4381 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-29 16:21:54 +00:00
ebanks 0d71dff928 Small bug fix to the new UG (need to initialize the entire posteriors array) means that we also get identical results as old UG when calling with 60 samples in the pilot1 data. Now that I'm happier with UGv2, I've transitioned it to use the correct AF priors instead of the busted ones still in the old UG. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4379 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-29 14:24:50 +00:00
hanna eee134baf2 Chris found a bug in the downsampler where, if the number of reads entering 
the pileup at the next alignment start is large, we don't add as many of those
incoming reads as we should.  No integration tests were affected.

Thanks, Chris!


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4378 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-29 11:18:12 +00:00
ebanks 0ec07ad99a Initial version of refactored Unified Genotyper. Using SNP genotype likelihoods and GRID_SEARCH AF estimation models, achieves the exact same results as original UG on 1-2 samples with the exception of strand bias (not implemented yet); other than that I have no idea. Needs tons more testing. Do not use. For Guillermo only. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4377 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-29 08:42:25 +00:00
kshakir 6df7f9318f For enums generate the full path to the Enum type to avoid collisions such as enum Model and enum Model used in the same class. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4376 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-29 05:28:59 +00:00
fromer e322e71c2f Restored SVN history for phasing 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4373 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-29 00:02:02 +00:00
fromer 720aaca8a0 Trying to restore SVN history for phasing 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4372 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-28 23:50:28 +00:00
fromer bf88117ead Trying to restore SVN history for phasing directory 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4371 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-28 23:48:24 +00:00
fromer dfb5143a41 Restore folder 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4370 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-28 23:46:07 +00:00
fromer 7c909bef82 Moved phasing classes out of playground! The code is still under production, though... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4369 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-28 23:21:28 +00:00
fromer 8d8980e8eb Fixed phasing algorithm to: 1. More correctly weed out irrelevant reads and sites; 2. Crudely flag sites with large phase discrepancies betweens reads 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4368 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-28 23:02:53 +00:00
chartl 5a5c72c80d Accidentally commited some debug output to PackageUtils, reverting change. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4367 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-28 21:58:42 +00:00
chartl 862c94c8ce Small change for Matt -- output partition types in lexicographic order. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4365 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-28 20:08:03 +00:00
ebanks 7ad87d328d Make sure to uppercase ref bases since they aren't coming from the engine 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4364 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-28 19:05:46 +00:00
bthomas 96cccafb0d Adding a few helper methods for accessing sample metadata, and associated unit tests. These are motivated by discussion with Ryan about how he'll use sample metadata in VariantEvalwalker - hopefully will make it easier for him. Methods are: 
-- getToolkit().subContextFromSampleProperty(): filters a VariantContext to genotypes that come from samples that have a given property value
-- getToolkit().getSamplesWithProperty(): gets all samples with a given property
-- getToolkit().getSamplesFromVariantContext(): sample objects that are referenced by name in a VariantContext



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4361 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-28 02:16:25 +00:00
ebanks 1034853a84 Adding 'solexa' to list of known/supported platforms 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4357 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-27 02:38:38 +00:00
aaron 70f03a7113 first pass of well-formatted tribble exceptions 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4352 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-25 03:29:33 +00:00
kshakir edaa278edd Removed cases where various toolkit functions were accessing GenomeAnalysisEngine.instance. 
This will allow other programs like Queue to reuse the functionality.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4351 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-25 02:49:30 +00:00
hanna 497bcbcbb7 Recent changes to the build system make the build system complain loudly about 
pieces of core that depend on playground.  Most of these have been eliminated by
(temporarily) promoting Aaron's report system to core in this checkin.  I'll 
follow up with other changes in separately.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4350 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-24 22:09:12 +00:00
hanna 6ebca5d219 Enhancements to build external projects for walker sharing. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4348 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-24 21:17:16 +00:00
corin eb1fa4bff3 changes an argument to an output so I can use it to track dependencies in queue 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4347 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-24 21:07:09 +00:00
depristo 745b8cc6d3 GATK now detects and UserExceptions when human lexicographically sorted data is provided 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4343 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-24 15:19:48 +00:00
rpoplin 1931b2e1bd Three fixes for VariantFiltrationWalker: Trying to filter an empty VCF file will produce a well-formed VCF file with zero records instead of a blank file, needed for pipelines. The first record's genotype info fields are now in the same order as all the others. The VCF header lines are pulled from just the input variant rod instead of from all rods. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4341 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-24 13:52:56 +00:00
kshakir 4ed9f437e9 Sliced the GAE in half like a gordian knot to avoid the constant merge conflicts. 
The GAE half has all the walker specific code.  The new "Abstract" GAE has the rest of the logic.
More refactoring to come, with the end goal of having a tool that other java analysis programs (Queue, etc.) can use to read in genomic data.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4339 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-23 23:28:55 +00:00
rpoplin 0c9fabb06f Fix in AnalyzeAnnotations, somebody changed it look for ID in the vc's info field. This dinosaur desperately needs integration tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4338 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-23 19:48:44 +00:00
hanna 0c781968fb Tried to do a bit of pre-commit refactoring and screwed it up. Fixed. 
Thanks to Ryan for identifying the problem.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4336 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-23 18:17:29 +00:00
depristo d081b9b352 Improvements to error messages about @Requires and @Allows 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4334 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-23 12:08:27 +00:00
hanna 7841b301c4 Added more diagnostics so that I have some idea of what a 'general' exception 
is.  Required to fix bug ZjhCJAdwhtFq1x54ZlmlN8pFNcbrRpdJ and similar.  We
might want to change this particular case to a ReviewedStingException after
we gain a bit more experience with it.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4333 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-22 21:32:01 +00:00
fromer 44ccfc3531 Updated Phasing algorithm + evaluation module to properly implement haplotypes [including homozygous genotypes]; Implemented dynamic window phasing model for LARGE increase in efficiency 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4332 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-22 21:29:58 +00:00
hanna 8f75d88519 Fix for GATK run report ids: 
mOVsxGfDiiSMxVs2PPTVjzYTVbizlD6e
  f9kUHUADFsZ0LiTGxRL5zPmq9kZcA4cQ
  8eGHWJFAlBVmgxwPi3sMd1RmiN2PwHOf
  iLhvHWveypKb2F8vKS5irHylc3pYvlOb
  HDttXKUMEVoPrvVeWrH7E0htxYyNydMx
plus a bit of cleanup of custom exceptions in the sharding system.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4330 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-22 19:49:25 +00:00
kshakir 20b38b38f3 Updated from SnakeYAML 1.6 to 1.7. 
Added a pipeline java bean and YAML utility to serialize java beans.
Added a getFirehosePipelineYaml.sh that can pull firehose data into the pipeline yaml file format.
Updated the fullCallingPipeline.q to begin using the pipeline yaml file format for bams and reference.
More changes to come as this code gets tested out in the fullCallingPipeline.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4329 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-22 19:47:49 +00:00
hanna fb5d595ef0 Disable VCF header output in the Beagle integrationtest. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4327 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-22 16:50:03 +00:00
hanna 0c99c97685 The engine now automatically adds the command-line arguments to the header of every VCF, unless -NO_HEADER is specified. 
Changed integration tests, adding the -NO_HEADER argument, for walkers that previously did not include the command-line
arg headers.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4326 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-22 15:27:58 +00:00
aaron 1af9ca6d45 enabling tests that now pass with the conitg length validation. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4325 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-21 22:20:50 +00:00
depristo 522830fb01 Support for --assume-single-sample in UG, better malformated bam exceptions, and ignoring out of order contigs in seqdictutils. All for the CG bam file 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4323 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-21 20:33:34 +00:00
aaron 3938d53738 one broken build short of the hat trick. Fixing the unix test which expects the sequence dictionary of the Tribble track to equal the reference; we actually return the sequence dictionary of the track iself, with each contig set to the length of the sequence dictionary contig entry. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4322 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-21 18:47:20 +00:00
aaron b968af5db5 The tribble indexes are now updated with correct sequence lengths for each contig they have in their sequence dictionary. Also clean-up in the RMD track builder. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4321 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-21 18:21:22 +00:00
aaron 2586f0a1ca fix for the build I broke - the original file got corrupted, which I replaced with a version that didn't have the header stripped off. Other integration tests passed, but this test relied on the header being stripped off. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4320 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-21 15:35:25 +00:00
rpoplin 547763b230 Better error message for Petr's null pointer exception. Also added an exception integration test because I'm certain this used to work. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4319 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-21 13:44:40 +00:00
depristo 8719dde59d Now prints out PASS when a variant is unfiltered 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4318 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-21 13:16:41 +00:00
delangel 205fc0b636 Cleanup: Use Tribble's version of createVariantContextWithPaddedAlleles (no real functional difference) to avoid duplicated code. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4315 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-20 19:53:30 +00:00
delangel a10cfe213b Small bug fix in simple indel genotyper: Likelihood of case where best haplotype pair was (REF,REF) was not computed correctly. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4314 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-20 17:04:39 +00:00
ebanks f5a30d0248 I just spoke to Andrey & Kiran (the original authors of these tools), and they voted to kill these in favor of Picard 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4313 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-20 13:27:35 +00:00
delangel f64b6fddc1 Major changes/improvements to indel genotyper: 
a) Redid way to compute path metrics in indel error model. Paper formulation where we have an anchor point in the alignemt between read and haplotype won't work in practice except in nice data sets that are perfectly indel-realigned and that are well mapped by aligner. New formulation doesn't assume this, and it's actually simpler and uses less code. It now resembles more a classic SW dynamic programming formulation but it still preserves the HMM probabilistic formulation. 
b) Added a programmable call threshold, set by command line.
c) Use now sample name from BAM file, remove -sampleName argument.
d) Simplify loop to compute read-haplotype likelihoods.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4311 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-19 23:47:31 +00:00
rpoplin c6351a11d6 Clearer logger output when not using by-hapmap 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4308 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-18 16:10:42 +00:00
rpoplin 7e58d8ed61 CombineVariants now outputs the command line in the VCF header. Added a new hidden argument to VR walkers called --NoByHapMapValidationStatus to turn off the by-hapmap dbsnp rod behavior. Very useful for experimenting with which sets to use as training data. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4307 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-18 16:06:50 +00:00
kshakir a3f31e5df0 When QScript writers use the RodBind, then the File version of the same argument should be optional, i.e. should not always try to output the file, which when unpopulated will be null. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4305 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-17 18:22:07 +00:00
bthomas c6c6d32b46 Quickly adding a new convenience method for retreiving a group of samples. The method is getSamples(Collection<String>) and returns a set of sample objects. There's also a test there. 
Ryan is using this to modify VCF code today...



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4303 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-17 15:55:17 +00:00
kshakir a898908918 The output BAM file optional arguments of compression and whether to write an index are not outputs themselves. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4302 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-17 15:35:54 +00:00
bthomas bc12055fcf Quick patch to fix the sample code. It wasn't actually initializing the sample data source, so I added a call to initializeSampleDataSource() in GenomeAnalysisEngine. I think there was just an error resolving the versions of GenomeAnalysisEngine 
Also added a new error message that I thought would be helpful...



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4301 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-17 14:05:26 +00:00
ebanks a10b2a00a5 Moving the util VariantContext 'modifying' routines into VC itself (as opposed to VCUtils) so that we can pass the genotype data directly into it and are no longer forced to decode the genotypes for no reason. This means that any walker that takes in a VCF and modifies the records without touching the genotypes never have to decode them. I've hooked this into the other two Variant Recalibrator walkers for Ryan. One side effect, though, is that we no longer can sort the sample names in the VCF (i.e. if the input VCF doesn't have samples in alphabetical order, then we used to sort them when writing a new VCF but no longer do that), because if we don't decode then we can't re-order the genotypes. I don't think this is a big concern given that the Unified Genotyper does emit sorted samples and that's the main source for most of the VCFs we use. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4300 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-17 07:09:58 +00:00
bthomas f66ef4626e Fixing two minor issues: 1) adding a new error message if the user adds a fasta file in a directory that doesn't exist; 2) renaming my sample unit tests so they actually run. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4299 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-16 20:45:51 +00:00
rpoplin 3a400e3dc0 Added CountCovariates integration test to ensure that it throws an exception if a variant mask isn't provided. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4298 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-16 19:18:38 +00:00
rpoplin 2eb5d9b2d2 CountCovariates makes sure that it sees a rod type that it expects for use as a variant mask (accepted types are dbsnp, vcf, and bed) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4296 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-16 18:53:42 +00:00
aaron de56568ce4 Adding the appropriate DbSNP file to the performance tests so they don't exception out. 
The exception: "org.broadinstitute.sting.utils.exceptions.UserException$CommandLineException: Invalid command line: This calculation is critically dependent on being able to skip over known variant sites. Please provide a dbSNP ROD or a VCF file containing known sites of genetic variation."


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4293 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-16 16:30:54 +00:00
aaron 782e0018e4 removal of most of the old GATK ROD system; also a fix for -Dsingle so we can again run just a single unit or integration test (single tests in tribble can be run with the -DsingleTest option now). More to come. 
*** Three integration tests had to change: ***

RecalibarationWalkersIntegrationTest:
One of the tests was using the interval as the snp track, and wasn't supplying a DbSNP track (for CountCovariates)

SequenomValidationConverterIntegrationTest:
relies on Plink ROD which we've removed.  

PileupWalkerIntegrationTest: 
we no longer have implicit interval tracks, so there isn't a rod name over the specified region.  Otherwise the same result.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4292 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-15 22:54:49 +00:00
delangel c604ed9440 Several improvements to new indel genotyper (more to come soon): 
a) Turns out previous change of centering haplotype around indel was a bad idea. Context to the left of indel is important but not as important as right one, because by definition all alleles start at the same location, so haplotype is the same to the left of indel regardless of allele. So, go back to having a constant size window to the left of event.
b) Expand reference context so we can test larger haplotypes.
c) Optimize computation of read likelihoods by doing them in linear array instead of in a matrix - no difference in biallelic sites but could be significantly faster in multiallelic sites.
d) Bug fix: read alignment wasn't being computed correctly if, a) we were at an insertion, b) read started right at the insertion, c) read CIGAR didn't include insertion - more of these corner conditions are lurking, so a revamped computation of how reads align to candidate haplotypes is in the works.
e) Add debug option not to use prior haplotype likelihoods.
f) Don't hard-code NA12878 for genotyping, now sample name is a required input argument.
g) Bug fix: if there are no reads covering a candidate indel event, just output NO_CALL (didn't notice this in HiSeq, but in P1 data it happens all the time). I need to add a confidence threshold for calling later on.






git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4291 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-15 21:53:08 +00:00
depristo fb6d7d19f9 Better window size error message 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4290 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-15 20:40:56 +00:00
rpoplin b5d2e299d2 Make it more clear what is going on with the by-hapmap validation status in the dbSNP rod 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4289 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-15 17:29:31 +00:00
rpoplin 0a06fbdb94 Adding header lines to output of VR walkers to settle validator warnings. Command lines are added to the VCF header. GATK version numbers will be added to the header lines by Matt. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4288 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-15 16:45:03 +00:00
depristo 41fa323e63 Added iterator for tribble, fixing GS bug report. Removed unnecessary tabix double wrapping. Intergation tests to ensure the BTI works with both vcfs and vcf.gz 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4287 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-15 16:38:04 +00:00
asivache d7b5baf8e5 Now uses tagging of -I arguments. Multiple -I options (merging) is now allowed. In somatic mode 'tumor' and 'normal' tags are required for each input bam, the order does not matter anymore (since we use tags!) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4286 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-15 13:58:51 +00:00
bthomas e5f81d25d4 Adding the --sample-metadata (-SM) command line argument and associated functionality. This is something Matt and I have been working on for a while. Basically, it allows you to integrate sample metadata into an analysis, by including a sample file. More detailed documentation is on the wiki: http://www.broadinstitute.org/gsa/wiki/index.php/Adding_Sample_data_to_an_analysis 
This commit adds two important classes: Sample, which contains data about one sample; and SampleDataSource, which manages sample data a la ReferenceDataSource and ReadsDataSource. 

This code should be stable, but it has not been integrated with existing walkers yet. That's the next commit. 

In the meantime, feel free to experiment with the code - there are two basic example walkers in the playground.sample package. And PLEASE let me know if you see any errors/inconsistencies.

Note that this also adds a new dependency on SnakeYaml, a YAML parser.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4285 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-15 11:50:22 +00:00
ebanks dd23f204ab Making the UG args that allow users to proceed with insufficient bam headers (no SM or PL tags) @Hidden; removed them from wiki. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4283 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-15 01:54:50 +00:00
ebanks 514b28210e Have VF write to sdout when no -o is supplied 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4282 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-15 01:48:33 +00:00
ebanks 1901e3208e Oops, ran integration tests before Guillermo committed his change to the Beagle code 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4281 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-15 01:41:02 +00:00
ebanks 4e83ba411f We now do lazy loading for the genotype data in VCF. Practically, almost all walkers end of loading the genotype data because we need to be smarter about transfering the unparsed genotype string when modifying VariantContexts; however, this does solve the problem for VR's piece to generate clusters (shaved off 75% of runtime for Ryan's large case). That further optimization will happen later. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4279 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-15 00:18:17 +00:00
depristo 74d4f124b1 Bug fixes to allow us to generate GATKRunReports for very early errors that leave the engine in a corrupt state. Vastly better error handling of common command line problems. Analysis output now notes whether an exception is a a UserException or a StingException 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4278 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-14 22:45:15 +00:00
delangel 2be5e862f1 forgot to commit change to MD5 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4277 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-14 19:28:03 +00:00
delangel 6d07181dc9 When processing Beagle output and creating new vcf, output the filtered records in the original input vcf as is, so that we don't lose the information on them when we run Beagle. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4276 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-14 19:18:45 +00:00
hanna 7fa6b2135b Added a back door so that integration tests can reset the sequence dictionary 
in the reference.  Reset routine is not accessible to any class outside
GenomeLocParser's package.

We'll have to do something more intelligent with this when the GATK goes
distributed.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4275 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-14 18:58:08 +00:00
depristo dbb641280e CycleCovariate now tolerates SOLEXA as machine type. Also, exception handling is now written to stderr. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4274 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-14 12:35:57 +00:00
ebanks 71d2d69b41 Better error message 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4273 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-14 05:04:26 +00:00
fromer 248cc308b2 ReadBackedPhasing silently ignores sites with ploidy != 2 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4272 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-13 21:14:17 +00:00
fromer 528f6344af Moved ReadBackedPhasingWalker to phasing sub-directory 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4271 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-13 19:36:41 +00:00
depristo fa3be2209f Improvements to the error display code to print out the SVN number in all messages. Fixes to CallableLoci and tests to check for that case 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4270 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-13 18:36:45 +00:00
depristo 4d0ff336c2 Missed update input 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4269 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-12 15:46:13 +00:00
depristo 7880863eb7 Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4267 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-12 15:07:38 +00:00
depristo 7ad8fbdd5a Moved GATKException to exceptions 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4266 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-12 14:47:19 +00:00
depristo 1876c9856a Moved stingexception 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4265 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-12 14:39:22 +00:00
depristo bccebf8899 Newly placed StingException 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4264 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-12 14:38:46 +00:00
depristo 3964e02fb6 Newly placed StingException 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4263 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-12 14:38:32 +00:00
depristo 595907e98e Moving StingException 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4262 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-12 14:34:15 +00:00
depristo 40e6179911 Penultimate step in exception system overhaul. UserError is now UserException. This class should be used for all communication with the USER for problems with their inputs. Engine now validates sequence dictionaries for compatibility, detecting not only lack of overlap but now inconsistent headers (b36 ref with v37 BAM, for example) as well as ref / bam order inconsistency. New -U option to allow users to tolerate dangerous seq dict issues. WalkerTest system now supports testing for exceptions (see email and wiki for docs). Tests for vcf and bam vs. ref incompatibility. Waiting on Tribble seq dict improvements to detect b36 VCF with b37 ref (currently cannot tell this is wrong. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4258 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-12 14:02:43 +00:00
delangel da2e879bbc Miscellaneous improvements to indel genotyper: 
- Add a simple calculation model for Pr(R|H) that doesn't rely on Dindel's HMM model. MUCH faster, at a cost of slightly worse performance since we're more sensitive to bad reads coming from sequencing artifacts (add -simple to command line to activate).
- Add debug option to calculation model so that we can optionally output useful info on current read being evaluated. (add -debugout to commandline).
- Small performance improvement: instead of evaluating haplotype to the right of indel (just with a 5 base addition to the left), it seems better to center the indel and to add context evenly around event.




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4257 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-12 13:50:28 +00:00
ebanks 61d511f601 Small memory performance improvement: remove the mapping from the hash instead of setting the value to null (i.e. remove the key too) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4256 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-12 05:19:09 +00:00
ebanks a0231f073f Damnit. Enabling the Picard code to recalculate all of the relevant SAMRecord attribute tags means that I need to have reference bases over all read bases even after realignment (and there are some big indels in dbsnp). Fortunately, I have my trusty IndexedFastaSequenceFile reader handy! Re-enabling the previously broken performance test. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4255 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-12 05:06:37 +00:00
hanna 87aca64716 Jumped the gun a bit on bam on-the-fly indexing -- Tim says it's not ready yet. 
Turned it off by default and added a property to turn it back on.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4254 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-10 21:16:03 +00:00
rpoplin 7b113a4886 Truncate the floating point numbers coming out of the variant recalibration walkers. Integration tests now work with both 1.6.0_16-b01 and 1.6.0_21-b06 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4253 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-10 18:37:49 +00:00
depristo 8f1a32acae All exceptions thrown by the GATK have been reviewed and UserErrors replaced where appropriate. Shazam. Another check-in will remove the GATKException and restore the StingException. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4252 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-10 15:25:30 +00:00
aaron cf33614ddc remove the test that's failing the performance tests, please don't release until this is figured out 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4251 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-10 06:30:40 +00:00
aaron 4adb07683d all fixed..thanks Matt! 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4250 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-10 06:18:59 +00:00
aaron bd4bc84abd comment out the broken aligner test again - I'll take a crack at fixing it tomorrow. Each software engineer is going to take a pass at fixing it, and we'll see who can do it with the most style. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4249 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-10 05:22:24 +00:00
rpoplin 61e848c4f0 It's clear from Sendu's calling and my own calling that -qScale 100.0 is a much better default value for low pass data. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4248 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-10 01:47:21 +00:00
hanna e183b6598c - Fix our private repository of bwa reference support files. 
- Update the test to point to our repository.
- Update the md5 to reflect new Picard tag ordering.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4247 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-10 00:29:26 +00:00
depristo 1de713f354 Massive review of maybe 50% of the exceptions in the GATK. GATKException is a tmp. tracker so that I can tell which StingExceptions I've reviewed. Please don't use it. If you are working on new code and are considering throwing exceptions, it's either UserError or StingException, please 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4246 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-09 23:21:17 +00:00
kshakir 4183e8805a Fixed reference (via busted symlink) /broad/1KG 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4245 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-09 20:34:51 +00:00
aaron f5c295b6b2 add a little bit of documentation to the RMD track builder and wrap any exceptions thrown in tribble with the file source and line that caused the error. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4243 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-09 17:56:36 +00:00
rpoplin aeb897db7f VR walkers look at by-hapmap validation status by default. Eric will be updating the syntax to allow for more flexibility here. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4242 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-09 15:40:56 +00:00
kshakir d7f55574e2 Re-enabling aligner integration test now that we're back to having more than 1 or 2GB memory. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4241 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-09 15:09:48 +00:00
rpoplin d625186796 I think the VR integration tests are fine. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4240 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-09 15:00:41 +00:00
depristo 6a30617a60 Initial implementation of UserError exceptions and error message overhaul. UserErrors and their subclasses UserError.MalFormedBam for example should be used when the GATK detects errors on part of the user. The output for errors is now much clearer and hopefully will reduce GS posts. Please start using UserError and its subclasses in your code. I've replace some, but not all, of the StingExceptions in the GATK with UserError where appropriate. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4239 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-09 11:32:20 +00:00
depristo ca9c7389ee Not useful 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4238 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-09 02:33:03 +00:00
depristo 8708753a6a checkin for removal 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4237 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-09 02:32:46 +00:00
hanna 5119bdb55e - Update DoC to support output to /dev/null. 
- Add a release sanity check for DoC.
- Update release sanity checks with new command-line argument system.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4236 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-08 23:43:18 +00:00
fromer 1b1ec7e52d Changed default phasing window size to 10 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4235 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-08 21:28:36 +00:00
fromer ce031b2f05 PhasingEvaluator prints out interesting sites (only 1 phased, or phases disagree) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4233 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-08 18:21:21 +00:00
ebanks 40283f6456 Success! TranscriptToGenomicInfo now works without the delicate hacks that Ben had put in. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4232 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-08 18:06:00 +00:00
ebanks cd091d7309 This walker can NOT be tree-reducible (in its current state). Given that it's meant to be run just once for any given transcript set, this is not at all a problem. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4231 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-08 16:47:51 +00:00
ebanks ae9cba1c73 After an epic battle with this code until 3am last night, I have discovered that it is tragically and fatally busted. Ben clearly didn't understand how the ROD system works when writing it and so it is unusable in its current state. I've ripped out all code and it now gracefully exits telling the user that we are actively working on a replacement for this tool. Sigh. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4230 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-08 16:39:41 +00:00
ebanks 29f7b1e6d6 Trivial update 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4229 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-08 14:02:38 +00:00
ebanks cd2bfb09ef Change for Tim: invalidate the MD tag (temporarily) if it exists in a read that gets realigned 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4228 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-08 13:59:09 +00:00
ebanks 65edbced36 Addition for Tim: recalculate the NM and UQ tags after realignment. Also, don't fix the insert size calculation, since that's done by fix mate information. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4227 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-08 04:02:14 +00:00
chartl 71046e650e Added a more robust check for Jishu -- am pretty sure the .bam header is busticated 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4223 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-08 01:11:22 +00:00
fromer ae3f7026a4 Corrected phasing quality evaluation to correctly account for hom sites that break phase 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4222 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-07 22:43:54 +00:00
hanna 501f6a0e14 Temporary hack to disable index creation when target BAM is /dev/null. Tim 
promises me that Picard will put in a real solution next week.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4220 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-07 16:57:51 +00:00
fromer 754c2c761e Added minimum phasing quality for phasing evaluation 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4219 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-07 14:29:11 +00:00
ebanks 5d0d9c7dce My parallel version of TranscriptToInfo now emits 'chr start end' instead of 'chr:start-end' for records so that 1) they can be easily sorted in coordinate order (allowing me to emit records out of order if I choose) and 2) the file can be tabix indexed (when we stop finding 'critical' bugs in that code). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4218 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-07 05:20:40 +00:00
ebanks 4d4ef5b42c In the end, it's not worth rewriting TranscriptToInfo from scratch. I'm keeping the old one around for a bit so I can play with this new version which 1. doesn't store the records in memory so can be run in under 1Gb of memory, 2. actually emits all of the records (the original fails in some cases), and 3. is refactored to cut out ~20% of the code. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4215 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-06 02:37:34 +00:00
kiran 0dd5a0990d Now annotates sites marked as filtered out (this is important if sites are in a lower-quality tranche). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4214 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-04 00:36:55 +00:00
delangel ef7454a241 Minor improvements to indel genotyper: 
a) Ability to specify haplotype size from command line
b) Expand reference context  window so we can form haplotypes for longer indel events.
c) small bug fix in temp output writer (to be removed once I can emit vcfs)



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4212 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-03 22:52:08 +00:00
depristo 7eeabe534a QSample walker for 1KG -- measures aggregate quality of sequencing. Includes misc. improvements throughtout the code, including using the new Tribble GenotypeLikelihoods class for working with VCF GLs from the UG 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4211 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-03 18:21:43 +00:00
rpoplin e3962c0d13 VR integration tests are longer but much more useful. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4210 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-03 15:50:19 +00:00
hanna da11efa1a2 Automatically write BAM file indices for coordinate-sorted BAMs. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4209 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-03 14:10:44 +00:00
fromer 529eecd4dc Added phasing sub-directory to keep walkers directory clean 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4208 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-03 13:38:46 +00:00
fromer c0ce9ca8cc Added phasing sub-directory to keep walkers directory clean 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4207 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-03 13:32:30 +00:00
rpoplin 60003aeaca Bug fix in VariantRecalibrator. Only add sample names from the input rod bindings, not from all rod bindings. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4206 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-03 13:31:49 +00:00
fromer c119f64514 Added phasing sub-directory to keep walkers directory clean 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4205 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-03 13:24:18 +00:00
depristo 3c9597d45a OnTraversalDone writes output to out now 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4203 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-03 12:55:03 +00:00
depristo 73d41bfa24 CountLoci nows writes out to a file for Queue status tracking. VariantAnnotatorEngine has a special group None that doesn't add any annotations; useful for those who are testing UG performance 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4202 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-03 12:52:33 +00:00
ebanks b59d62927e Fix busted performance test (-outputBam has been deprecated in the BQ recalibrator in favor of -o) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4201 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-03 12:51:53 +00:00
hanna 70bb480939 The battle is over. Picard is revved. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4200 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-03 05:28:01 +00:00
ebanks fdaac4aa78 As the VCF guru, I'll take this one for Andrey. Someone has actually found a deletion at the beginning of the chromosome. Instead of failing with an ArrayIndexOutOfBoundsException, just don't try to print out the record. Our VCF writer doesn't really support this case (yet). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4199 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-03 03:27:43 +00:00
ebanks c45ffcdaed Changing documentation (temporarily) to warn people that -U is not supported. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4198 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-03 03:18:07 +00:00
delangel 8a7f5aba4b First more or less sort of functional framework for statistical Indel error caller. Current implementation computes Pr(read|haplotype) based on Dindel's error model. A simple walker that takes an existing vcf, generates haplotypes around calls and computes genotype likelihoods is used to test this as first example. No attempt yet to use prior information on indel AF, nor to use multi-sample caller abilities. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4197 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-03 00:25:34 +00:00
fromer a1cf3398a5 Added basic version of phasing evaluation: GenotypePhasingEvaluator 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4196 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-02 22:09:50 +00:00
kshakir fd5970fdd4 At chartl's superb suggestion, command line files are now all Files instead of old method of sometimes "has a File". Should be easier when reassigning them. 
No longer generating deprecated GATK arguments on the Queue extensions.
Emitting deprecation warnings to Queue compile to help debugging issues.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4195 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-02 21:30:48 +00:00
rpoplin 0bb05fb472 Bug fix in VariantRecalibrator. Only add sample names from the input rod bindings, not from all rod bindings. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4194 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-02 21:12:09 +00:00
chartl 3a4844ebde Additional partition types into DepthOfCoverage: 
- Sequencing Center
- Platform
- Sample by Center
- Sample by Platform
- Sample by Platform by Center <---- needed for analysis I'm doing

The fact that the latter three needed their own partition types, rather than being dictatable from the command line, combined with the new hierarchical traversal types, and new output formatting engine, suggest that DepthOfCoverageV3 is about ready to be retired in favor of a newer, sleeker version.

For now, this will do.
 


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4193 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-02 19:30:03 +00:00
chartl 590bb50d16 Test for missing read group 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4192 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-02 14:22:13 +00:00
kiran acd6bd2430 Experimental tool to annotates indels that are provided in a VCF file based on RefGene. Specifies gene, transcript, strand, type (Non-frameshift, frameshift, 5'-UTR, 3'-UTR, SpliceSiteDisruption, Intron, or Unknown). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4191 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-01 23:30:28 +00:00
hanna dc5f858d29 Replaced placeholder support for splitting by read group with read support (sorry everyone), and added relatively comprehensive unit tests to ensure that splitting by read group works. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4190 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-01 22:24:50 +00:00
rpoplin b28f63a948 Base recalibrator now uses -o and deprecates -outputBam 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4189 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-01 22:13:50 +00:00
kshakir 33400074fa Updated tribble BED parsing code to use the official UCSC spec, and updated tests to match expected results. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4188 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-01 21:49:06 +00:00
depristo 995cfe34fe You can have an error so early that some engine fields are uninitialized. Commit protects RunReport from these errors 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4185 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-01 19:00:25 +00:00
rpoplin a975db2c2e Bug fix for the case of reads with no read bases! 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4184 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-01 16:58:54 +00:00
rpoplin 469bbaa240 Added more integration tests for the variant quality score recalibrator 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4181 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-01 15:31:24 +00:00
depristo 8c4009ee18 Oops, don't enable reporting in integration tests 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4179 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-31 22:56:18 +00:00
rpoplin 5b94c926c8 More precise language. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4178 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-31 21:44:22 +00:00
rpoplin 96040726ac Better exception text for the common error of providing only dbsnp but giving dbsnp sites zero clustering weight. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4177 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-31 21:36:43 +00:00
depristo 32c6b48106 Proper memory metrics in the file. Please use -et if at all possible 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4175 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-31 20:30:09 +00:00
chartl 63c7cbd89b Forgot to commit this long ago, change so the tables are correctly propagated 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4174 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-31 19:06:52 +00:00
aaron db4ff7317f allowing empty RMD files (we need to not validate their sequence dictionaries against the reference in this case) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4173 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-31 17:45:33 +00:00
ebanks 3d6c4fc55f Removing the obsolete --hapmap and --hapmap_chip options 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4172 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-31 16:57:05 +00:00
depristo b33873206a GATKRunReport now has an ID (random 32 char string) that uniquely identifies the JOB run and can be used to find a run in the run repository 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4171 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-31 16:18:57 +00:00
ebanks 3c956110f3 Fixing up the VCFWriter storage code: instead of assuming all samples are coming from the input bam file (they're not), just use the original VCF header for writing the temporary thread files. Now parallelization in e.g. the Genomic Annotator works. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4168 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-31 02:16:07 +00:00
aaron 69d92fab4f adding the ability to get iterators from Tribble without having an index, and updating the Tabix code to the latest Samtools SVN version (this still doesn't fix the outstanding tabix bugs, waiting for Heng on that). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4167 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-30 21:49:23 +00:00
fromer 50f7f18cbd Changed ReadBackedPhasing default PQ threshold to 10 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4166 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-30 21:26:15 +00:00
chartl e64d1be475 Check if VC is null before trying to subset it (can happen with indels) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4165 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-30 20:43:37 +00:00
depristo 1ddb5d17c9 hostname now fully qualified and working 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4163 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-29 17:04:37 +00:00
depristo 4c28fc3a39 Clear documentation for GATKRunReport 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4161 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-29 15:59:25 +00:00
kiran 16b75e3b9a A new version of the ErrorRateByReadPosition walker, using the GATKReport functionality to store and emit its output. This version of the walker is roughly half the number of lines as the previous version, owing simply to the removal of all of the output formatting that's now handled by GATKReport. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4160 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-29 05:41:13 +00:00
kiran fd19c63aaf A data structure that allows data to be collected over the course of a walker's computation, then have that data written to a PrintStream such that it's human-readable, AWK-able, and R-friendly (given that you load it using the GATKReport loader module). 
This object designed to be both the structure that holds data during the execution of the walker, as well as the object that properly formats and emits the data so that it can be easily loaded into R.  In the end, you get a table that looks like this:

##:GATKReport.v0.1 ErrorRatePerCycle : The error rate per sequenced position in the reads
cycle  errorrate.61PA8.7         qualavg.61PA8.7
0      0.007451835696110506      25.474613284804366
1      0.002362777171937477      29.844949954504095
2      9.087604507451836E-4      32.87590975254731
3      5.452562704471102E-4      34.498999090081895
4      9.087604507451836E-4      35.14831665150137
5      5.452562704471102E-4      36.07223435225619
6      5.452562704471102E-4      36.1217248908297
7      5.452562704471102E-4      36.1910480349345
8      5.452562704471102E-4      36.00345705967977
...

A GATKReport object can hold multiple tables, and the write() method will emit all tables in succession.  Each table starts with its own ##:GATKReport.v0.1 table header, so each table can stand alone.  This allows for tables to be mixed and matched in a single file, or for the output from different walkers to be combined into a single file with no ill effect.

The display property of individual columns can be turned off.  This is useful when a column is used to store intermediate results, necesary for the computation of some later value, but the contents of the intermediate column itself are not required in the final output file.

Finally, the GATKReportTable allows for some simple, mathematical, element-wise and column-wise operations.  For instance, two whole columns can be divided, the results of the operation being stored in a third column.  This mimics the most basic of R operations, where whole vectors can be added, subtracted, multiplied or divided without requiring the developer to explicitly write a loop.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4159 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-29 05:39:24 +00:00
ebanks df76474b34 Proper filtering when indels are being lifted over 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4158 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-29 04:48:31 +00:00
depristo 3fd2392090 Improved interface to getting command line options. Now fully traverses all objects to get all internal argument collections. Preliminary (but disabled version) of phoning home (see -et argument for more information). Captures correct and erroring out runs and writes out gzipped, xml report with lots of useful information. Needs a bit more information but is approximately working. Reports going to /humgen/gsa-hpprojects/GATK/reports/ in submitted directory that will be collated by some external tool. Only operating if -et STANDARD or -et STDOUT are provided currently and REPORT_DIR contains a file called ENABLE. WalkerTest now adds -et NO_ET to tests to avoid populating the reports with tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4155 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-28 22:53:32 +00:00
rpoplin 9c3f403307 Add the calculated lod value to the info field of each recalibrated VCF record. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4153 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-27 21:33:58 +00:00
delangel fe19539188 Small bug fix: if a read falls at the edge of an indel event (but is not part of it), don't count it towards consistency computation. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4152 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-27 20:37:27 +00:00
rpoplin 54355b1864 In variant quality score recalibrator Preserve the definition of known and novel to be presence in dbSNP or not even when training with 1KG project calls. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4151 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-27 19:07:59 +00:00
ebanks 7a5f297083 actually modify the vcf when a sample has been down-sampled 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4150 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-27 19:03:21 +00:00
ebanks 9860db64a3 Fix up liftover to enable lifting over indels 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4148 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-27 17:55:27 +00:00
hanna fb177c4fee If only dcov is specified, assume that selected downsample type is BY_SAMPLE. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4147 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-27 17:35:41 +00:00
ebanks 9584cbc05e UG now downsamples to 250x by default 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4146 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-27 16:53:15 +00:00
ebanks 431392330e Re-enable the max records in ram argument, which I accidentally removed 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4145 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-27 16:42:49 +00:00
hanna de5ccfb0b1 Moved hasPileupBeenDownsampled() based on Eric's request. Also eliminated 
@Deprecated constructors from AlignmentContext.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4142 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-27 16:12:05 +00:00
ebanks 427a2f85e9 The Indel Realigner now lets the engine do all of the setup for args affecting the SAM writer. Thanks, Matt! 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4141 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-27 15:19:47 +00:00
asivache a3d9d23b0f Now prints het genotype with GQ=0 for each indel; in two-sample (normal-tumor) mode, prints both genotypes (N and T) as hets for germline events or hom ref for N and het for T for somatic events (all genotypes still have GQ=0) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4140 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-27 15:06:42 +00:00
ebanks dda84a0e54 Re-enabling indels for the Genomic Annotator as per Steve's patch. Steve assures me that he will test this out really well. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4139 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-27 15:01:25 +00:00
hanna 6f4af47aac setMaxRecordsInRam now a member of StingSAMFileWriter. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4138 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-27 14:50:41 +00:00
ebanks bfcac33e80 Cleaning up playground utils and tests 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4136 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-27 01:25:47 +00:00
ebanks 4979dcc9a7 Finishing up the playground cleanup (for now) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4135 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-27 01:19:37 +00:00
ebanks 0452b1ab68 archiving, removing, or promoting to core from playground 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4134 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-27 01:07:42 +00:00
hanna d773b3264b Eliminated -mrl option. 
Eliminated -fmq0 option.
Eliminated read group hallucination.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4133 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-26 21:38:03 +00:00
depristo f384d4a5d6 A java reimplementation of vcf2table in python; supports getting more useful information about genotypes (HET, e.g.) than was possible in python. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4130 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-26 17:50:33 +00:00
asivache 1e193e4c20 prinring '\n' at the end of line leads to some aesthetical advantages 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4129 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-26 16:29:42 +00:00
asivache 9b3ffa5f64 Now outputs VCF (as standard output associated with -o)! Can also outptut, in parallel, a lightweight bed and fully annotated .txt (old verbose format) with --bed and --verbose, respectively 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4128 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-26 16:26:03 +00:00
ebanks dfae48cee0 Moving supported tools to core 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4127 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-26 13:56:19 +00:00
ebanks 45d895dcf4 Remove the check in the Unified Genotyper for hitting the max reads at locus value. Instead, simply add a flag to the INFO field if any of the samples has been downsampled. 95% hooked up. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4126 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-26 05:50:47 +00:00
ebanks e06b2c90ef Cap the default size of join tables; this can be modified with the --maxJoinTableSize argument. Also, misc cleanup of the comments. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4125 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-26 05:21:26 +00:00
ebanks 79cd716671 More cleanup of the Genomic Annotator. Also, we now require join tables to have unique entries for the column keyed on the join. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4124 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-26 04:43:52 +00:00
ebanks dd7f136298 Office-mate courtesy: fixing Andrey's busted integration test 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4123 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-26 02:00:06 +00:00
kshakir 0105e8d063 Updated Queue GATK generation to reflect -B and -I changes. 
To add support for "-I:tumor tumor.bam", the GATK argument
import_file (-I) is now generated as a List of NamedFile objects.
Could not get sugar working 100%.  To activate sugar import the
gatk package.  This effectively adds a new method to java.io.File
called toNamedFile.  When adding a file to the list call
  countReads.import_file :+= myJavaFile.toNamedFile
See scala/qscript/examples for actual examples.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4122 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-25 22:17:36 +00:00
hanna bdb3a7ebe6 The tagger was automatically combining identical tags, but this is a problem 
for the ROD system.  Eliminate tag combine operation.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4121 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-25 22:01:32 +00:00
fromer 39da567d48 Changed ReadBackedPhasing to be a RodWalker (corrected to By(READS)) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4120 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-25 20:53:04 +00:00
ebanks 4678613893 Significant fixes for the Genomic Annotator. 
1. Rip out all of Ben's code intended to circumvent the stable VCF Writer output system in multi-threaded mode (I threw up a little when 
I saw this code).  This will improve memory consumption when running with -nt.
2. Don't annotate indels or > bi-allelic sites.
3. Fix bug where not all records were making it into the output VCF.
4. General code clean up.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4118 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-25 20:16:50 +00:00
fromer 41e53d37e1 Changed ReadBackedPhasing to be a RodWalker (more efficient, since it is ROD-focused) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4117 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-25 19:43:57 +00:00
rpoplin ac58eb3cbb Slightly better error message for the common error of only providing a dbsnp track but giving it zero clustering weight. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4114 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-25 18:41:21 +00:00
rpoplin 5623e01602 GenerateVariantClusters and VariantRecalibrator now uses hapmap and 1kg ROD bindings (in addition to dbsnp) to distinguish between knowns and novels. It no longer looks at by-hapmap validation status so providing hapmap is highly recommended. Example on the wiki. Input variants tracks now must start with input. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4113 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-25 18:33:40 +00:00
hanna bf0b6bd486 Update integration tests to use the new ROD syntax. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4112 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-25 18:13:30 +00:00
asivache 14198b74d5 Can now compute av. qualities and stddevs per cycle for both original (when present in bam) and recalibrated quals 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4111 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-25 17:14:58 +00:00
asivache 23dbaa68e6 Can design assays when multiple (distinct) events occur at the same locus (one assay per event) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4110 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-25 16:52:47 +00:00
ebanks b4baa3eb8f Cleanup. INDELS model is now disconnected (and renamed 'DINDEL' in preparation for adding plumbing for Guillermo soon) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4106 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-25 14:52:51 +00:00
hanna 3dc78855fd Command-line argument tagging is in, and the ROD system is hacked slightly to support the new syntax 
(-B:name,type file) as well as the old syntax.  Also, a bonus feature: BAMs can now be tagged at the
command-line, which should allow us to get rid of some of the hackier calls in GenomeAnalysisEngine.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4105 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-25 03:47:57 +00:00
fromer aa8cf25d08 Implemented fully symmetric sliding window read-backed phaser 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4104 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-24 21:12:32 +00:00
ebanks cba5f05538 Small fixes for consistency in the numbers. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4103 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-24 20:48:25 +00:00
rpoplin 7bbd67f3c4 Fixing stray comments. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4102 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-24 20:19:39 +00:00
rpoplin 85007ffa87 Some clean up for the variant recalibrator. Now uses @Input and @Output so that it can join the Queue party. Users now specify a -o, -clusterFile, -tranchesFile, and -reportDatFile. Example on the wiki. ApplyVariantCuts now has an integration test. Base quality recalibrator now requires a dbsnp rod or vcf file. Now that the base quality recalibrator is using @Output the PrintStream shouldn't be closed in OnTraversalDone. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4101 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-24 20:14:58 +00:00
delangel f2b138d975 Small refactoring: make Haplotype a public class since it will be soon extended and shared with other callers. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4100 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-24 17:52:36 +00:00
ebanks 43f1fb2380 Okay, finally done with VCF compression. Now: 
1. Uses blocked gzip compression.
2. No more -bzip option available (since we can't compress to sdout).
3. Only file extensions that are compressed are .gz and .gzip.
4. No more need for CompressedVCFWriter.java



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4099 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-24 16:36:54 +00:00
ebanks 25fb53e7a2 Oops, forgot to call toLowerCase(). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4097 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-24 14:43:24 +00:00
ebanks 7957b60768 We now automatically compress the output VCF if the file suffix is one of the supported types (.gz, .bz, .bz2). You can still specify -bzip if you want to use another file suffix (or pipe it to sdout for some reason). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4096 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-24 14:39:59 +00:00
rpoplin 7a8b6b87da Committing Michael Yourshaw's patch for AnalyzeCovariates. We spawn each RScript process and wait for it to finish in series. Thanks Michael! 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4095 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-24 13:06:25 +00:00
ebanks 9fb151f417 Minor update 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4094 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-24 05:17:10 +00:00
ebanks 44f3c5639a I have finally figured out that when you volunteer to do something in group meeting, you keep getting pestered about it on Mark's Omniplan doc until it gets done (except for contig aliasing, of course). As such... 
We can now emit bzipped VCFs from the GATK.

Details: any walker that defines a VCFWriter for its @Output (i.e. pretty much every core walker from UG and on), also has associated with it the -bzip (--bzip_compression) boolean argument.  When set, it will emit a VCF that is compressed with bzip2.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4093 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-24 04:14:50 +00:00
hanna 691333f75c Force isRequired() to be false for @Deprecated args. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4092 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-23 23:50:30 +00:00
hanna 5d6a6420a9 New behavior for filling it output streams: if required==true for a field and the field 
is an output stream, we'll automatically create it and point it to stdout.  Otherwise, 
we'll leave it empty.  
I think about it like this: marking a field 'required' indicates to the GATK that the 
walker author requires a value for this field, and if the GATK can provide one without 
end user intervention, it will.  Maybe this is hackish.  We'll try it and see.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4091 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-23 23:39:13 +00:00
ebanks 90aef66ec5 Minor fixes for my last commit 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4090 348d0f76-0448-11de-a6fe-93d51630548a
 2010-08-23 23:25:29 +00:00