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Author SHA1 Message Date
ebanks c7a8dffa89 Check for division by 0 in annotations 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2539 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-07 19:27:15 +00:00
depristo 076481f786 Fixes to mergeVCF -- now correctly supports merging of filter fields. Also removed incorrect hasFilteringCodes() function. Updated intergration tests 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2535 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-07 14:50:13 +00:00
rpoplin cea544871d Fixed an issue with recalibrating original quality scores above Q40. There is a new option -maxQ which sets the maximum quality score possible for when a RecalDatum tries to compute its quality score from the mismatch rate. The same option was added to AnalyzeCovariates to help with plotting q scores above Q40. Added an integration test which makes use of this new -maxQ option. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2534 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-07 13:50:30 +00:00
rpoplin 0a6bd5a270 CycleCovariate is now one-based so that 0 and -0 don't collide with each other. Solid recal modes now only change the inconsistent base and the previous base (along the direction of the read) instead of both the bases before and after. Removed estimatedNumberOfBins from the Covariate interface because it wasn't being used. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2498 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-04 20:52:15 +00:00
ebanks ed2fff13aa -Misc improvements to VCF code 
-Small fix to callset concordance


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2497 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-04 02:28:47 +00:00
ebanks b668d32cf1 Updated the min mapping quality and min base quality defaults to be 10 in both cases (and updated all integration tests) as suggested by Mark. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2494 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-03 21:31:04 +00:00
asivache ad549eacfd Now that we changed how deletions are represented, got to update MD5... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2491 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-30 22:00:58 +00:00
asivache 9c41ac252f Disable testSingleBPFailure - getReferenceContext() now whould agree to accept length > 1 genome locs as its argument, so there's nothing to test... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2486 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-30 21:12:00 +00:00
asivache 4aeb50c87d Added: integration test for extended pileup (with indels included) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2481 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-29 23:02:23 +00:00
rpoplin 96c4929b3c Recalibrator now uses NestedHashMap instead of NHashMap. The keys are now nested hash maps instead of Lists of Comparables. These results in a big speed up (thanks Tim!). There is still a little bit of clean up to do, but everything works now. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2474 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-29 21:01:32 +00:00
ebanks 5fdf17fccb Removed the VCF "NS" annotation (which wasn't working for pooled calls anyways) since it's ambiguous and not useful. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2465 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-29 17:30:47 +00:00
aaron a34c2442c0 moved hard-coded file paths to the oneKGLocation, validationDataLocation, and seqLocation variables setup in the BaseTest. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2460 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-29 07:40:48 +00:00
depristo fcc80e8632 Completely rewritten duplicate traversal, more free of bugs, with integration tests for count duplicates walker validated on a TCGA hybrid capture lane. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2458 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-28 23:56:49 +00:00
alecw b5e5e27225 New versions of picard-private, sam and picard jars for TileCovariate and regeneration of NM tag 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2456 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-28 22:18:55 +00:00
rpoplin 562db45fa5 Sites that were marked NO_DINUC no longer get dinuc-corrected but are still recalibrated using the other available covariates. Solid cycle is now the same as Illumina cycle pending an analysis that looks at the effect of PrimerRoundCovariate. Solid color space methods cleaned up to reduce number of calls to read.getAttribute(). Polished NHashMap sort method in preparation for move to core/utils. Added additional plots in AnalyzeCovariates to look at reported quality as a function of the covariate. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2451 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-28 20:19:37 +00:00
ebanks 12990c5e7a Added qual-by-depth annotation 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2445 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-25 02:30:30 +00:00
ebanks 438d21842a The new recalibrator had been mimicking the behavior of the old one in that if there was no dinuc available (following a no-call base or at either end of a read), it didn't try to recalibrate. Now that Ryan has modularized the system, we no longer need to skip the base completely (we just need to skip the dinuc value)... which is good because the Picard people complained after realizing that cycle #1 never got recalibrated. 
The major effects of this commit are as follows:
1. We no longer skip any good bases (of course, this change alone breaks every single integration test).
2. The dinuc covariate returns a "no dinuc" value for the first base of a read (but not for the last base anymore, since there is a valid dinuc) or if the previous base is a bad base (e.g. 'N').

I've done a bunch of testing on real data and everything looks right; however, let's wait until the recalibrator guru gets back from vacation next week and can double-check everything before shipping this out in another early access release.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2443 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-24 20:41:29 +00:00
ebanks 6df40876a3 Un-reverted Matt's previous changes and fixed integration tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2441 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-24 02:47:00 +00:00
hanna 2bd0b1bbf7 After further review, it's unclear that my patch in RecalDataManager was the right choice. Reverting. 
Also updating other IntervalCleanerIntegrationTest failures that were masked by my first patch.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2440 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-24 00:32:33 +00:00
hanna 98c268483e Fixed issues with the integration tests: 
1) sam-jdk apparently no longer supports custom tags with type int[] values.
2) BAM output for indel cleaner integration test changed in a way that's so subtle it can't be seen after converting the output to .sam.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2439 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-23 23:12:22 +00:00
ebanks 770093a40e Oops - forgot to check this one in. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2433 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-23 19:53:28 +00:00
ebanks dc96879861 2 separate changes which both affect lots of UG integration md5s, so I'm committing them together: 
1. allele balance annotation is now weighted by genotype quality (so we don't get misled by borderline het calls)

2. Updates to the Unified Genotyper for parallelization:
   a. verbose writing now works again; arg was moved from UAC to UG
   b. UG checks for command that don't work with parallelization
   c. some cleanup



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2432 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-23 19:03:56 +00:00
ebanks 872a9d1c7b I'm making this change now (as opposed to waiting until Monday) to honor Tim's request. 
The cycle covariate is now first/second of pair aware.  I'm taking it on faith from both Chris Hartl (waiting on slides from him) and Tim that this is the right thing to do.  We'll have Ryan confirm it all next week.
The only change is that if a read is the second of a pair, we multiple the cycle by -1 (a simple way of separating its index from that of its mate).
Of course, this broke all integration tests.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2431 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-23 16:26:43 +00:00
ebanks 87e5a41964 Fixed a bug that accounted for a bunch of my remaining mis-cleaned indels. 
Also, slightly optimized the cleaner by using readBases (instead of readString) and caching cigar element lengths.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2419 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-21 05:46:16 +00:00
aaron 7e0f69dab5 Changed the GLF record to store it's contig name and position in each record instead of in the Reader. Integration tests all stay the same. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2410 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-18 22:54:56 +00:00
hanna 80b3eb85fa Fixed curiously epic failure in read-backed pileup: size() mismatched the numReads-numDeletions at that locus in the case where includeReadsWithDeletionsAtLoci == false, causing failures including bad output from pileup walker. Also fixed up ValidatingPileup to run with the new ReadBackedPileup instead of just compiling successfully. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2409 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-18 22:52:44 +00:00
rpoplin fdf542c214 The CycleCovariate for 454 data is now the TACG flow cycle. That is, each flow grabs all the T's, A's, C's, and G's in order in a single cycle. This is changed from incrementing the cycle whenever there is a discontinuous nucleotide along the direction of the read. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2408 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-18 22:39:51 +00:00
ebanks 1cde4161b7 Fixed another test 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2399 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-18 05:05:03 +00:00
ebanks 94f5edb68a 1. Fixed VCFGenotypeRecord bug (it needs to emit fields in the order specified by the GenotypeFormatString) 
2. isNoCall() added to Genotype interface so that we can distinguish between ref and no calls (all we had before was isVariant())
3. Added Hardy-Weinberg annotation; still experimental - not working yet so don't use it.
4. Move 'output type' argument out of the UnifiedArgumentCollection and into the UnifiedGenotyper, in preparation for parallelization.
5. Improved some of the UG integration tests.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2398 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-18 04:14:14 +00:00
rpoplin 6fbf77be95 Updating the two solid_recal_mode options to also change the previous base since solid aligner prefers single color mismatch alignments over true SNP alignments. COUNT_AS_MISMATCH mode has been removed completely. The default mode is now SET_Q_ZERO. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2394 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-17 20:07:26 +00:00
hanna 07f1859290 Added integration test for running the recalibrator with no index. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2393 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-17 19:10:53 +00:00
ebanks c75ec67f84 When called as a standalone, VariantAnnotator now emits samples in sorted (as opposed to random) order in VCFs. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2392 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-17 19:01:08 +00:00
hanna b863fffdf6 Fix 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2390 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-17 17:55:00 +00:00
asivache e6cc7dab26 fixing md5 sum; new version of IndelIntervalWalker does the right thing... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2388 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-17 01:04:13 +00:00
ebanks b626fc0684 Joint Estimate is now the default calculation model. 
Reworked all of the integration tests so that they're now more comprehensive, cover more of what we wan to test, and don't take forever to run.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2376 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-16 19:41:02 +00:00
ebanks bb312814a2 UG is now officially in the business of making good SNP calls (as opposed to being hyper-aggressive in its calls and expecting the end-user to filter). 
Bad/suspicious bases/reads (high mismatch rate, low MQ, low BQ, bad mates) are now filtered out by default (and not used for the annotations either), although this can all be turned off.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2373 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-16 17:28:09 +00:00
ebanks 874552ff75 Pull the genotype (and genotype quality) calculation out of the VCF code and into the Genotyper. 
[Also, enable Mark's new UG arguments]



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2355 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-15 04:29:28 +00:00
rpoplin 8e44bfd2ef CycleCovariate and PrimerRoundCovariate now correctly handle negative strand 454 and SOLID reads. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2349 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-14 21:52:30 +00:00
ebanks bd2a46ab4c I want to move over to hpprojects tonight, so I'm checking in various changes all in one go: 
1. Initial code for annotating calls with the base mismatch rate within a reference window (still needs analysis).
2. Move error checking code from rodVCF to VCFRecord.
3. More improvements to SNP Genotype callset concordance.
4. Fixed some comments in Variation/Genotype



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2341 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-13 02:52:18 +00:00
ebanks 2ea7632b76 The SNP genotype concordance module is now more comprehensive. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2330 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-11 18:34:33 +00:00
ebanks 2de7e1a178 Move VariantAnnotator over to use a StratifiedAlignmentContext split by sample. 
The only major difference is that we are now able to get accurate allele balance ratios.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2321 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-11 05:28:28 +00:00
ebanks f7c44ad019 - Read in arguments for the header based on reflection 
- Hook up Variation and Genotype in SSG



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2300 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-09 21:35:33 +00:00
ebanks 40c2d7a4bc Fix all-bases-mode and genotype-mode in the UG and add integration tests for them. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2295 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-09 17:41:30 +00:00
ebanks 4e54b91ce4 UG now outputs the FORMAT header fields when there's genotype data. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2294 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-09 16:31:07 +00:00
ebanks fb900b12e1 VariantFiltration now details the filters it has used in the header of the VCF it produces. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2292 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-09 15:36:15 +00:00
ebanks 8a1c876104 Weird. I thought I had updated these md5s... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2289 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-09 03:31:41 +00:00
ebanks 717eb1de96 - Depth annotation now includes MQ0 reads 
- Removed MQ0 annotation
- Updated RMS MQ annotation to use new pileup
- UG now outputs all of its arguments as key/value pairs in the header (for VCF)
- Cleaned up VCFGenotypeWriterAdapter interface a bit



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2288 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-09 02:53:00 +00:00
ebanks e8822a3fb4 Stage 3 of Variation refactoring: 
We are now VCF3.3 compliant.
(Only a few more stages left.  Sigh.)



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2287 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-08 21:43:28 +00:00
rpoplin 1d5b9883db Added --solid_recal_mode argument to experiment with different ways of dealing with solid reference bias. Currently the default option is DO_NOTHING which means use the same behavior as the old recalibrator. Eventually the new methods in RecalDataManager will be moved over to a SolidUtils class. Added transition and transversion methods to BaseUtils that work like simpleComplement, used with the color space in my solid methods. Also, initial check-in of HomopolymerCovariate. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2276 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-07 14:26:27 +00:00
ebanks c0528cd88e Updated the CallsetConcordance classes to use new VCF Variation code... and uncovered a whole bunch of VCF bugs in the process. I'm not convinced that I got them all, so I'll unit test like crazy when the refactoring is done. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2272 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-06 11:43:40 +00:00
ebanks 08f2214f14 Stage 1 of massive Variation/Genotype refactoring. 
This stage consists only of the code originating in the Genotyper and flowing through to the genotype writers.  I haven't finished refactoring the writers and haven't even touched the readers at all.

The major changes here are that
1. Variations which are BackedByGenotypes are now correctly associated with those Genotypes
2. Genotypes which have an associated Variation can actually be associated with it (and then return it when toVariation() is called).

The only integration tests which need to be updated are MSG-related (because the refactoring now made it easy for me to prevent MSG from emitting tri-allelic sites).



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2269 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-06 03:12:41 +00:00
ebanks 861221d046 - Moved various header line printing into a single method 
- Fixed output for coverage above min depth



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2254 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-04 02:15:43 +00:00
ebanks c2017cc91b PrintCoverageWalker functionality moved to DepthOfCoverageWalker. Added integration tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2247 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-03 17:23:59 +00:00
ebanks 01cf5cc741 1. Merged CoverageHistogram into DepthOfCoverageWalker 
2. Fixed bug in histogram calculation for small intervals
3. Better output in DoCWalker
4. Comments added to code



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2245 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-03 17:01:53 +00:00
ebanks 44b9f60735 PercentOfBasesCovered functionality moved to DepthOfCoverageWalker. Added integration tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2244 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-03 16:11:09 +00:00
ebanks a88202c3f6 Refactored DoCWalker to output in a more helpful and usable style. It now outputs in tabular format with 2 different sections: per locus and then per interval. 
I am now at a point where I can merge the functionality from other coverage walkers into this one.
Thanks to Andrew for input.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2239 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-03 05:28:21 +00:00
ebanks 0a2304eff8 - Rename minConfidenceScore in VariantEval to minPhredConfidenceScore 
- Moved validation walkers to new qc dir
- Killed unused test



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2218 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-02 17:59:19 +00:00
ebanks 7055a3ea2d - All annotations are now required to return their VCF INFO keys and descriptions 
- Renamed keys to fit with the standard naming
- FisherStrand is no longer standard
- Integration tests no longer test experimental annotations since they're not stable



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2216 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-02 17:24:06 +00:00
depristo 6231637615 fixes for VariantAnnotations and second bases. Misc. removal of failing (and unstable) integration tests that require rereview 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2213 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-02 15:41:35 +00:00
rpoplin 3180fffd43 Eliminated unnecessary boxing of longs in RecalDatum. Changes to RecalDatum in preparation for new AnalyzeCovariates script. Updated TableRecalibrationWalker to make use of these changes. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2199 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-01 16:49:05 +00:00
chartl 21a9a717e4 Some minor changes and test: 
- DepthOfCoverage is now by reference (so locus-by-locus output correctly reports zero-coverage bases)
  - VariantsToVCF now lets you bind variants with any string except intervals and dbsnp (not just NA######)
  - A PileupWalker integration test on a particularly nasty FHS site
  - Two second-base annotation related integration tests on that same site
       + outputs were all hand-validated in matlab; within a certain tolerance for the annotations




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2197 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-01 15:15:54 +00:00
rpoplin d8146ab23d Changed the format of the recalibration csv file slightly so that it is easier to load the file into something like R and look at the values of the covariates. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2183 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-30 17:55:23 +00:00
depristo 75b61a3663 Updated, optimized REadBackedPileup. Updated test that was breaking the build -- it created a pileup from reads without bases... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2169 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-25 23:30:39 +00:00
ebanks d0f673f0c0 Use Math.abs so we don't get (inconsistent) -0's 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2160 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-25 19:08:34 +00:00
rpoplin 6ff8526592 Added arguments to the recalibration walkers so the user can specify the default read group id and platform to use when a read has no read group. There are also options to force every read group and every platform to be the specified values. Added integration tests that use a bam file with no read groups. Added comments to all the covariates to explain what each of the methods in the Covariate interface are used for. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2157 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-25 15:41:12 +00:00
ebanks e1e5b35b19 Don't have the spanning deletions argument be a hard cutoff, but instead be a percentage of the reads in the pileup. Default is now 5% of reads. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2155 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-25 04:54:44 +00:00
depristo 03342c1fdd Restructuring and interface change to ReadBackedPileup. We now lower support the Pileup interface, the BasicPileup static methods, and the ReadBackedPileup class. Now everything is a ReadBackedPileup and all methods to manipulate pileups are off of it. Also provides the recommended iterable() interface of pileup elements so you can use the syntax for (PileupElement p : pileup) and access directly from p.getBase() and p.getQual() and p.getSecondBase(). Only a few straggler walkers use the old style interface -- but those walkers will be retired soon. Documentation coming in the AM. Please everyone use the new syntax, it's safer, and will be more efficient as soon as the LocusIteratorByState directly emits the ReadBackedPileup for the Alignment context, as opposed to the current interface. In the process of the change over, discovered several bugs in the second-best base code due to things getting out of sync, but these changes were resolved manually. All other integrationtests passed without modification. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2154 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-25 03:51:41 +00:00
rpoplin c9ff5f209c Added a CountCovariates integration test that uses a vcf file as the list of variant sites to skip over instead of the usual dbSNP rod. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2152 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-24 21:51:38 +00:00
ebanks 3484f652e7 1. Variation is now passed to VariantAnnotator along with the List of Genotypes so non-genotype calls has access to all relevant info. 
2. Killed OnOffGenoype
3. SpanningDeletions is now SpanningDeletionFraction



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2151 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-24 21:47:20 +00:00
rpoplin dffa46b380 BAM files created by TableRecalibration now have the version number and list of covariates used appended to their header with a new 'PG' tag. Eventually the entire list of command line args will be put in there as well. Big thanks to Matt and Aaron. The integration test uses the --no_pg_tag so that the md5 doesn't change every time the version number changes. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2148 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-24 20:53:57 +00:00
ebanks b3f561710f Optimizations: 
1. Only do calculations in UG for alternate allele with highest sum of quality scores (note that this also constitutes a bug fix for a precision problem we were having).
2. Avoid using Strings in DiploidGenotype when we can (it was taking 1.5% of my compute according to JProfiler)

UG now runs in half the time for JOINT_ESTIMATE model.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2141 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-24 16:27:39 +00:00
ebanks 36d493e645 All standard annotations now inherit from StandardVariantAnnotation. Users can specify whether they want all annotations, just the standard annotations, or specific annotations. When calling in from another walker, the default is just the standard ones. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2134 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-24 03:55:12 +00:00
ebanks ee5093d2c6 -Added VariantFiltration integration tests 
-Added integration test for GLFs



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2133 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-24 02:36:27 +00:00
chartl 6a52ca3db6 Update to the UG integration test. Why I had to rm -rf my entire sting directory to get it to correctly fail we may never know. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2128 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-23 21:23:00 +00:00
chartl 23983b2fd8 New annotation: ResidualQuality 
Computes a metric for how much error is left that isn't explained by ref or snp bases. This is the sum of Q scores, weighted by the proportion of non-ref non-snp bases to non-snp bases. Reported in Log space.

Update to the integration test so bamboo doesn't look as though someone murdered it with a spork




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2124 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-23 20:04:01 +00:00
ebanks 70059a0fc9 Refactored joint estimation model to allow subclasses to overload PofD calculation over all frequencies. Pooled model now takes only 20% of time that it used to. 
Added integration test for pooled model and updated other joint estimation tests to be more comprehensive now that they are faster.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2123 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-23 20:03:38 +00:00
rpoplin 7f947f6b60 Updated recalibrator integration tests to use all three platforms as well as a bam with multi-platform reads intermingled. CountCovariates v2.0.1: Once again uses a read filter to filter out zero mapping quality reads. Added --sorted_output option to output the table recalibration file in sorted order 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2122 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-23 19:51:36 +00:00
ebanks c299ca5f49 It would help if I copied the MD5s from the right integration test... 
I hate Mondays.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2121 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-23 17:21:36 +00:00
ebanks ff4797acbb Forgot to check in integration test update 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2120 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-23 17:13:51 +00:00
rpoplin 1d46de6d34 The old recalibrator is replaced with the refactored recalibrator. Added a version message to the logger output. These walkers start at version 2.0.0 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2117 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-23 14:58:33 +00:00
ebanks bf935a6ab1 1. Fixed bug in PrimaryBaseSecondaryBaseSymmetry code (not checking for null before trying to access object's methods) which was causing Integration Tests to fail. 
2. Retired allele frequency range from UG, which wasn't very useful.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2113 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-23 01:31:48 +00:00
ebanks d84444200b The Unified Genotyper now sorts the sample names in the vcf that it outputs. 
[There was no reason to enforce that every VCF being output from the GATK should have the samples sorted, since someone might want them ordered non-alphabetically]


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2102 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-20 16:13:18 +00:00
rpoplin 22aaf8c5e0 Added the old recalibrator integration tests to the refactored recalibrator sitting in playground. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2096 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-19 22:43:28 +00:00
aaron 6ba1f3321d Fixed the sample mix-up bug Kiran discovered, and added a unit test in the VCF reader class (Thanks for the good example files Kiran). Also renamed the toStringRepresentation function to toStringEncoding, and added a matching method in VCFGenotypeRecord. 
Updated the integration tests that were failing to due to different ordering of genotyping entries in VCF, I'll check in the VCF diff tool I wrote when I get a cycle or two.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2092 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-19 18:17:47 +00:00
chartl 90212c643b more effective & efficient test for SecondBaseSkew 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2075 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-18 20:53:32 +00:00
ebanks 0a35c8e0ba 1. The joint estimation model now constrains genotypes to be AA,AB,or BB only (i.e. to use a single alternate allele). Note that this doesn't work for the old models (point estimate or SSG) because calculations aren't divided by alternate allele. 
2. Allele frequency spectrum is not emitted for single samples (since it doesn't make sense).
3. If in pooled mode, throw an exception of pool size isn't set appropriately.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2072 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-18 17:43:15 +00:00
depristo 6fe1c337ff Pileup cleanup; pooled caller v1 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2070 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-18 17:03:48 +00:00
chartl 539f6f15e5 Added -- 
Second base skew annotations and integration tests. Nothing need be given except -A SecondBaseSkew; the statistic it annotates calls with is a chi-square statistic given by the deviation of the observed proportion of reference second-best-bases from the expected 1/3. Future additions may be to ask that the deviation be instead from a given transition table.

A big note for all users: All IllegalStateExceptions from the variation ROD (e.g. the RodGeliText) are dealt with SILENTLY. I understand this isn't optimal, but I'd rather simply not annotate a non-bi-allelic site than fail completely (there are quite a few such sites even on the regions over which the integration test has been written).




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2064 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-18 00:11:13 +00:00
ebanks 4d9c826766 Integration tests actually run on real data now. 
<tries to hide sheepish grin>


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2061 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-17 21:04:14 +00:00
ebanks 5e126875ea temporarily disable (tests are broken) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2060 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-17 20:45:52 +00:00
ebanks a048f5cdf1 -Refactored JointEstimation code so that pooled calling will work 
-Use phred-scale for fisher strand test
-Use only 2N allele frequency estimation points



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2059 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-17 20:21:15 +00:00
ebanks 4558375575 Stage 1 of the VariantFiltration refactoring is now complete. There now exists a parallel tool called VariantAnnotator which simply takes variant calls and annotates them with the same type of data that we used to use for filtering (e.g. DoC, allele balance). The output is a VCF with the INFO field appropriately annotated. 
VariantAnnotator can be called as a standalone walker or by another walker, as it is by the UnifiedGenotyper.  UG now no longer computes any of this meta data - it relegates the task completely to the annotator (assuming the output format accepts it).

This is a fairly all-encompassing check in.  It involves changes to all of the UG code, bug fixes to much of the VCF code as things popped up, and other changes throughout.  All integration tests pass and I've tediously confirmed that the annotation values are correct, but this framework could use some more rigorous testing.

Stage 2 of the process will happen later this week.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2053 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-16 02:41:20 +00:00
ebanks bf451873ff 1. Bug fix: check that AF=0 doesn't contain more probability than 1-fraction 
2. Fix for Kiran: allow UG to call SNPs at deletion sites; we'll add an annotation to the VariantAnotator for deletions at the locus (next week).
3. Added integration tests for joint estimation model



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2038 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-13 18:02:18 +00:00
hanna 7c386fa428 Another case of reordering of read groups blowing up checksums. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2030 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-13 00:07:35 +00:00
hanna 8145ed4672 Take 2, updating picard with bug fix for bam files containing no reads. 
Just stomped on the existing md5s because that's what Eric told me to do.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2029 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-12 22:52:08 +00:00
aaron c3c001e02e cleanup of the traversal output code 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2026 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-12 06:18:10 +00:00
ebanks 6a37090529 Output changes for VCF and UG: 
1. Don't cap q-scores at 99
2. Scale SLOD to allow more resolution in the output
3. UG outputs weighted allele balance (AB) and on-off genotype (OO) info fields for het genotype calls (works for joint estimation model and SSG)


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2011 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-10 16:31:31 +00:00
depristo d316cbad4c VariantFilteration now accepts a VCF rod in addition to an input geli. It will then annotate this VCF file with filtering information in the INFO field too. --OnlyAnnotate will not write in filtering output 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2008 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-10 13:24:58 +00:00
aaron 2ed423ed56 print the current location in read walkers (in addition to the number of reads processed), along with some refactoring to support the change. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2006 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-10 05:57:01 +00:00
ebanks c9c3cf477a Based on feedback from Kiran, we know uniquify sample names as sample.rodName (instead of sample.1, sample.2, ...) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2005 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-10 02:41:37 +00:00
ebanks 2fa2ae43ec Enough people have found this useful, so... 
Moving Callset Concordance tool to core and adding integration test.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2003 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-09 20:59:18 +00:00
ebanks 6fdfc97db6 Added optional field DP to VCF output for Mark. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1981 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-06 20:03:22 +00:00
aaron aacd72854f a fix for a bug Andrey discovered: in read-based interval traversals we're dupplicating reads in rare cases. The problem was that to accomidate a bug in SAM JDK indexing, we were forced to add one to the stop of our QueryOverlapping() calls to ensure we always got all of the overlapping reads. 
Added a PlusOneFixIterator that wraps other iterators, and eliminates reads that start outside of our intended interval (interval stop - 1).  Updated and checked BamToFastqIntegrationTest MD5 sums.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1976 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-05 05:26:33 +00:00
ebanks 11d950abe0 No longer allow the lod_threshold argument - use confidence instead. 
Have UG output qscores in all cases.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1968 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-03 16:18:51 +00:00
ebanks 2b96b2e4e7 better multi-sample integration test 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1933 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-29 13:51:51 +00:00
ebanks 3091443dc7 Sweeping changes to the genotype output system, as per several discussions with Matt & Aaron. 
Some things still need to be changed, but it will entail some more design decisions first (which means I get to bug M&A again tomorrow!).


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1930 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-29 03:46:41 +00:00
aaron 3fb3773098 a fix for traverse dupplicates bug: GSA-202. Also removed some debugging output from FastaAltRef walker 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1912 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-26 20:18:55 +00:00
aaron ad1fc511b1 intermediate commit for some changes in the Variation system, so Eric can go ahead with his changes. Everything is pretty set, but the Variation interface could use a convenience method that joins all the alternate alleles. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1903 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-23 06:31:15 +00:00
aaron cfa86d52c2 ensure that in the indel case we don't allow identification as both an insertion and deletion at the same location in the VCF ROD 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1875 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-19 18:21:00 +00:00
ebanks bb180a23ef Updated MD5 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1871 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-18 05:30:38 +00:00
ebanks b9e8867287 -push allele frequency and genotype likelihood variable definitions down into the subclasses so that they can use different data structures 
-use slightly more stringent stability metric
-better integration test



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1869 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-18 04:22:17 +00:00
aaron 41a95cb3f0 fixing unified genotyper test for change: VCF output now emits no calls as ./. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1865 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-16 19:38:58 +00:00
ebanks 07b134a124 Added some integration tests for multiple samples 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1861 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-16 15:22:10 +00:00
aaron a69ea9b57c Cleaning up the VCF code, adding lots of tests for a variety of edge cases. Two issues are still outstanding: updating the no call string with the standard 1000g decided on today, and fixing Eric's issue where not all the VCF sample names are present initially. 
also: their, I hope your happy Eric, from now on I'll try not to flout my awesomest grammer in the future accept when I need to illicit a strong response :-)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1858 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-16 04:11:34 +00:00
aaron eb90e5c4d7 changes to VCF output, and updated MD5's in the integration tests 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1836 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 18:42:48 +00:00
ebanks d89bc2c796 This class no longer outputs in sequenom format 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1832 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 17:16:36 +00:00
ebanks 0c06bf9dbc Explicitly set output to GELI now that default is VCF 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1824 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-13 22:12:03 +00:00
aaron 98e3a0bf1a VCF can now be emitted from SSG. The basic's are there (the genotype, read depth, our error estimate), but more fields need to be added for each record as nessasary. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1797 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-08 19:50:04 +00:00
ebanks df8ea8f437 UG integration test. This was the old SSG test with MD5s updated. 
I'll need to add some multi-sample tests in a bit...


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1791 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-08 17:43:58 +00:00
ebanks 008455915a One way of making the integration test stop failing is to remove it... 
[waiting for Matt to cringe...]


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1789 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-08 17:08:41 +00:00
ebanks 04fe50cadd *** We no longer have a separate model for the single-sample case. *** 
For now, a single sample input will be special-cased in the EM model - but that will change when the EM model degenerates to the single sample output with a single sample as input.  For now, the EM code for multi-samples isn't finished; I'm planning on checking that in soon.

The SingleSampleIntegrationTest now uses the UnifiedCaller instead of SSG, and so should all of you.  More on that in a separate email.
Other minor cleanups added too.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1785 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-08 14:08:57 +00:00
aaron f9a0eefe4b GELI_BINARY is now functional, and can be used as a variant type in SSG (-vf=GELI_BINARY). Also fixed the max mapping quality column in both GELI output formats, we haven't been correctly outputing up until now. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1774 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-07 18:20:34 +00:00
aaron 7fc4472e6d A big fix for MergingSamRecordIterator, where we weren't correctly handling the comparisons of SAMRecords correctly (we weren't applying the new reference index first, so sometimes the MT contig would be ID 23, sometimes 24 in different records). 
Also a fix to the GLF tests, and a correction to PrintReadsWalker to remove the close() on the output source, the source handles that itself (and you get a double close).

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1758 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-02 19:35:35 +00:00
ebanks 7249fade05 updated 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1756 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-02 18:10:34 +00:00
aaron 2e4949c4d6 Rev'ing Picard, which includes the update to get all the reads in the query region (GSA-173). With it come a bunch of fixes, including retiring the FourBaseRecaller code, and updated md5 for some walker tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1751 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-30 20:37:59 +00:00
hanna 70e1aef550 Better integrate the @ArgumentCollection into the command-line argument parser. Walkers can now specify their own @ArgumentCollections. Also cleaned up a bit of the CommandLineProgram template method pattern to minimize duplicate code. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1746 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-29 22:23:19 +00:00
aaron d262cbd41c changes to add VCF to the rod system, fix VCF output in VariantsToVCF, and some other minor changes 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1715 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-24 15:16:11 +00:00
ebanks b0fa19a0b2 Fixed recal integration test 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1689 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-22 20:22:32 +00:00
ebanks 6780476fb5 updated to deal with new dbSNP rod 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1687 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-22 19:46:32 +00:00
aaron 7bfb5fad27 fixing the dbSNP test. Also removing unnessasary comments from the GenomeLocParser, added some tests, and commented out the performance test 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1676 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-21 23:32:24 +00:00
asivache a6bd509593 Changing the carpet under your feet!! New incremental update to th eROD system has arrived. 
all the updated classes now make use of new SeekableRodIterator instead of RODIterator. RODIterator class deleted. This batch makes only trivial updates to tests dictated by the change in the ROD system interface. Few less trivial updates to follow. This is a partial commit; a few walkers also still need to be updated, hold on...

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1667 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-21 16:55:22 +00:00
aaron 7b39aa4966 Adding the VCF ROD. Also changed the VCF objects to much more user friendly. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1658 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-18 20:19:34 +00:00
hanna 01a9b1c63b Fix for problem where err stream remapped to output stream in certain cases, (hopefully) completing Matt's hat trick of fail. Thanks, unit tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1634 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-16 08:33:56 +00:00
aaron eedf55e94d temp fix for a broken test, we'll fix the test tomorrow. We promise, we're engineers, we love our tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1633 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-16 04:36:42 +00:00
aaron b401929e41 incremental clean-up and changes for VariantEval, moved DiploidGenotype to a better home, and fixed a spelling error. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1624 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-15 04:48:42 +00:00
ebanks 6783fda42a Updated unit test to reflect changes to vcf output 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1623 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-15 01:56:08 +00:00
aaron e03fccb223 Changes to switch Variant Eval over to the new Variation system. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1611 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-14 05:34:33 +00:00
aaron 5b41ef5f70 rod DBSNP had a bug where the reference wasn't calculated correctly under certain conditions. Fixed getRefBasesFWD and getRefSnpFWD so that they were more in line with getAltBasesFWD and getAltSnpFWD. Also updated Variant Eval tests to reflect this change. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1609 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-13 23:48:58 +00:00
depristo 6e13a36059 Framework for ROD walkers -- totally experiment and not working right now 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1600 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-12 19:13:15 +00:00
ebanks e24c8d00d5 So, the VCF spec allows for an optional meta field in the header representing the date. However, using this field means that integration tests run on the vcf file will fail the MD5 test (which is what happened to the VariantFiltration test this morning after working just fine yesterday). 
After consulting our resident expert (Aaron), we're going to (temporarily) remove the date from the vcf output until we can come up with a better solution.  However, this shouldn't cause any short-term problems because the data truly is optional.
VF test's MD5s are updated.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1580 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-10 14:28:43 +00:00
aaron 5a64a80ab5 changes to the variation class, updates to SSG, updated tests based on changes to the SSGenotypeCall, and added the ability to run a single integration test from using the build script. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1577 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-10 04:31:33 +00:00
ebanks 1362a56227 Added fasta tests and small fix to cleaner test 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1575 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-10 03:13:11 +00:00
ebanks 8ca89279aa Added a test for VariantFiltration and the VECs 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1574 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-10 02:21:14 +00:00
ebanks bed646e4f6 Adding cleaner test 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1561 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-09 16:05:56 +00:00
depristo d9588e6083 bug fixes to LIBS and LIBH following ultra-aggressive regression testing across 454, solid, and solexa 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1558 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-09 15:36:12 +00:00
aaron 0df6a9da5c -Seperating out normal (unit) tests and integration tests. From now on if your test are more of an integration test (i.e. you're testing a walker and all the subunits it relies on) please name the test "______IntegrationTest.java" instead of "______Test.java". 
-Bamboo will now run the integration tests once a day, and the normal units tests on each check-in.

-Also added a bunch of unit tests for VariantEval walker

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1555 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-09 15:01:40 +00:00
depristo eeb9b6eb13 GenotypeLikelhoods now support a cache per subclass, avoiding genotyping clashes 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1554 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-09 10:39:14 +00:00
ebanks 0cc219c0df -Added unit test for walkers dealing with intervals for cleaning 
-I also uncovered a corner case in the cleaner that for some reason was commented out but shouldn't have been.  Hooray for unit tests!



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1553 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-09 02:35:17 +00:00
depristo ec0f6f23c7 LocusIterationByState is now the system deafult. Fixed Aaron's build problem 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1552 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-09 01:28:05 +00:00
depristo 1c3d67f0f3 Improvements to the CountCovariates and TableRecablirator, as well as regression tests for SLX and 454 data 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1539 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-04 22:26:57 +00:00
depristo 2b0d1c52b2 General WalkerTest framework. Includes some minor changes to GATK core to enable creation of true command-line like GATK modules in the code. Extensive first-pass tests for SSG 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1538 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-04 19:13:37 +00:00
aaron 0cc634ed5d -Renamed rodVariants to RodGeliText 
-Remove KGenomesSNPROD
-Remove rodFLT
-Renamed rodGFF to RodGenotypeChipAsGFF
-Fixed a problem in SSGenotypeCall
-Added basic SSGenotype Test class
-Make VCFHeader constructors public

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1536 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-04 18:40:43 +00:00
depristo a08c68362e Renaming error to getNegLog10PError(); added Cached clearing method to GL; SSG now has a CallResult that counts calls; No more Adding class to System.out, now to logger.info; First major testing piece (and general approach too) to unit testing of a walker -- SingleSampleGenotyper now knows how many calls to make on a particular 1mb region on NA12878 for each call type and counts the number of calls *AND* the compares the geli MD5 sum to the expected one! 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1530 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-04 12:39:06 +00:00
depristo 49a7babb2c Better organization of Genotype likelihood calculations. NewHotness is now just GenotypeLikelihoods. There are 1, 3, and empirical base error models available as subclasses, along with a simple way to make this (see the factory). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1481 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-30 19:16:30 +00:00
depristo 8e129d76fd Support for original quality scores OQ flag. pQ flag in TableRecalibation to preserve quality scores below a threshold (defaulting to 5) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1474 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-28 14:14:21 +00:00
depristo 37a9b84276 corresponding test 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1470 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-28 00:17:42 +00:00
hanna ccdb4a0313 General-purpose management of output streams. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1454 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-23 00:56:02 +00:00
aaron d101c20b30 added the ability to pass in a csv file of ROD triplets (one triplet per line) to the -B option 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1412 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-11 22:10:20 +00:00
aaron d69ae60b69 fixed two tests affected by my previous commit 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1408 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-11 17:57:50 +00:00
hanna dd228880ed Partially implemented NewHotnessGenotypeLikelihoodsTest caused the tests to fail. 
Ouch!  So hot it burned me.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1403 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-10 20:45:44 +00:00
depristo a864c2f025 Updated polarized reference priors, need DiploidGenotypePriors class that is directly used by the NewHotness genotypelikelihoods, more bug fixes and refactoring, etc. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1390 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-07 19:00:06 +00:00
depristo bbd7bec5db Continuing cleanup of SSG. GenotypeLikelihoods now have extensive testing routines. DiploidGenotype supports het, homref, etc calculations. SSG has been cleaned up to remove old garbage functionality. Also now supports output to standard output by simply omitting varout 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1387 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-05 22:25:30 +00:00
hanna 48713e154c Windowed access to the reference. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1383 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-05 16:29:15 +00:00
hanna 21d1eba502 Cleaned division of responsibilities between arguments to map function. Reference has been changed 
from an array of bases to an object (ReferenceContext), and LocusContext has been renamed to reflect
the fact that it contains contextual information only about the alignments, not the locus in general.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1376 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-04 21:01:37 +00:00
aaron bca894ebce Adding the intial changes for the new Genotyping interface. The bullet points are: 
- SSG is much simpler now
- GeliText has been added as a GenotypeWriter
- AlleleFrequencyWalker will be deleted when I untangle the AlleleMetric's dependance on it
- GenotypeLikelihoods now implements GenotypeGenerator, but could still use cleanup

There is still a lot more work to do, but this is a good initial check-in.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1335 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-29 19:43:59 +00:00
hanna 7a13647c35 Support for specifying SAMFileReaders and SAMFileWriters as @Arguments directly. *Very* 
rough initial implementation, but should provide enough support so that people can stop
creating SAMFileWriters in reduceInit.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1332 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-29 16:11:45 +00:00
hanna 2db86b7829 Move the cleaned read injector test from playground to core. Remove CovariateCounterTest's dependency on the CleanedReadInjector. Start doing a bit of cleanup on the CLP's FieldParsers. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1312 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-24 19:44:04 +00:00
aaron 0b16253db3 an iterator to fix the problem where read-based interval traversals are getting duplicate reads because reads span the two intervals. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1305 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-23 23:59:48 +00:00
aaron b4adb5133a GLF rod as a AllelicVariant object. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1282 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-21 00:55:52 +00:00
aaron 9ecb3e0015 adding GLFRods with tests and some other code changes 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1251 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-15 15:30:19 +00:00
aaron d86717db93 Refactoring of the traversal engine base class, I removed a lot of old code. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1209 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-09 21:57:00 +00:00
hanna da4d26b1ea Enum support for command-line argument system, and some cleanup for hacks to the CleanedReadInjector that were required because Enum support was missing. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1199 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-08 20:26:16 +00:00
hanna 433ad1f060 Cleanup...deprecate FastaSequenceFile2 in favor of IndexedFastaSequenceFile or ReferenceSequenceFile from Picard, depending on the application. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1196 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-08 18:49:08 +00:00
hanna d8fbb2b62c Refactoring; make a better home for the MalformedReadFilteringIterator. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1194 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-08 16:54:20 +00:00
aaron f6a273a537 other fixes for some broken unit tests 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1181 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-07 05:53:13 +00:00
aaron 033bafe7a1 fixed sam by reads test for the new filtering code 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1180 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-07 05:45:50 +00:00
depristo b9d533042e Two-tailed HardyWeinberg test implemented. VariantEval now separate violations from summary outputs for clarity; Fixing problems with CovariateCounterTest and TabularRodTest 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1177 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-06 22:02:04 +00:00
aaron bc17ff567a When you get the reference string for a read that is mapped partially off the end of a contig, the string is masked with X's for base positions without corresponding reference positions. Now with a test case! 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1156 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-02 14:15:50 +00:00
hanna 9b182e3063 Prep for documenting command-line arguments: delete some arguments that don't make sense any more given 
the state of the traversals and GATK input requirements: all_loci (replaced by walker annotation), max
OTF sorts (bam files must be sorted and indexed), threaded io (replaced by data sharding framework).


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1144 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-01 18:23:35 +00:00
aaron 03f8177a53 When you get the reference string for a read that is mapped partially off the end of a contig, the string is masked with X's for base positions without corresponding reference positions. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1121 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-29 20:51:55 +00:00
aaron 1dcababad1 a fix to make the test run 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1120 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-29 20:24:32 +00:00
depristo 5289230eb8 Version 0.2.1 (released) of the TableRecalibrator 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1108 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-25 22:50:55 +00:00
hanna ad3a3aa350 First pass at passing lists of files / lists of interval arguments work. Note that the interval 
ROD system will throw up its hands and not deal with intervals at all if multiple interval files 
are passed in (see JIRA GSA-95). 


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1105 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-25 20:44:23 +00:00
aaron 0a16519aa2 a couple of additions to the tests, plus a change to the artificial resource pool to support the queryContained flag 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1099 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-25 18:30:32 +00:00
aaron 5b1c23a7f2 changes to fix and test the interval based traversals 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1095 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-25 17:54:15 +00:00
hanna ef546868bf Pooling of unmapped reads -- improves runtime of files with tons of unmapped reads by an order of magnitude. 
Desperately needs cleanup.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1080 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-23 23:48:06 +00:00
aaron bcb64d92e9 Aaron: 1, GenomeLoc: 0. I changed our GenomeLoc class, seperating the creation of a genome loc (with the reference setup) to a parser class. GenomeLoc now just represents the actual genomic postion. The constructors are now package-protected (to enforce using the parser), but we may want to expose some constructors in the future. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1069 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-22 14:39:41 +00:00
depristo 8ac40e8e2d Updated version of the recalibration tool 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1060 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-19 17:45:47 +00:00
aaron 6ee64c7e43 added changes to support alec toUnmappedRead seek. Huge improvements (orders of magnitude) in unmapped read performance. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1021 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-16 22:15:56 +00:00
ebanks 647b8a1ab0 Fix TabularROD printing and testing so Aaron stops nagging me. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1016 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-16 15:49:26 +00:00
hanna 71e3825fa1 First pass of a walker for Eric that searches through an input BAM file for unclean reads, injecting the cleaned reads in their place and outputting the composite result. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@989 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-11 20:18:13 +00:00
aaron 63b5c12cbd Changed dataSources to datasources, to be consistant with the rest of our package names. Also, this makes me champion in the largest check-in contest. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@985 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-11 18:13:22 +00:00
aaron 195b4ea7b4 a rename for consistancy of Sam to SAM, creating a genotype utils dir, and moving the GLF code into it. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@984 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-11 17:46:06 +00:00
aaron ec2f015447 fixed a bunch of comments and license headers. 
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 2009-06-10 14:10:46 +00:00
hanna dc6a9ca196 Pooling resources to lower memory consumption. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@962 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-10 13:39:32 +00:00
aaron 36c98b9d6c added tools to test read based traversals using the artificial in-memory SAM file tools, and testing of the PrintReadsWalker 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@957 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-10 01:52:25 +00:00
aaron a8a2d0eab9 added support for the -M option in traversals. 
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 2009-06-08 15:12:24 +00:00
depristo 819862e04e major restructuring of generalized variant analysis framework. Now trivally easy to add additional analyses. Easy partitioning of all analyses by features, such as singleton status. Now has transition/transversional bias, counting, dbSNP coverage, HWE violation, selecting of variants by presence/absense in dbs. Also restructured the ROD system to make it easier to add tracks. Also, added the interval track -- if you provide an interval list, then the system autoatmically makese this available to you as a bound rod -- you can always find out where you are in the interval at every site. Python scripts improved to handle more merging, etc, into population snps. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@918 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-05 23:34:37 +00:00
aaron 109bef6c08 We're no longer in the read-dropping business. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@901 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-04 22:37:51 +00:00
hanna 5e8c08ee63 Update to latest version of picard. Change imports in all classes dependent on picard public from import edu.mit.broad.picard... to import net.sf.picard... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@849 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-28 20:13:01 +00:00