80af0f2f54
Changed the OUTPUT_BAM_FILE argument from String to SAMFileWriter and removed the call to close().
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2551 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-10 03:45:54 +00:00
7893aaefe9
Updates to chunk iteration. Includes the return of the dreaded *2.java files;
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hopefully I can find a way to kill these off before the Picard patch is ready.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2550 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-08 20:20:56 +00:00
fcce77c245
Added -beagle option to emit likelihoods file for use with the BEAGLE imputation engine; still experimental.
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(Also converted getPileup -> getBasePileup)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2549 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-08 18:41:04 +00:00
9cbae53ee1
Bug fixes for both SET_Q_ZERO and REMOVE_REF_BIAS solid recal modes regarding proper handling of negative strand reads. These changes yield a minor improvment in HapMap sensitivity.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2548 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-08 15:19:22 +00:00
dfcd5ce25b
Fixed broken test
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2547 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-08 06:13:01 +00:00
d5ab002449
Curiously, it seems I never set the default base quality used by the Genotyper to 10. It's done now.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2546 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-08 06:02:01 +00:00
b468369dfa
-UG's call into VariantAnnotator now uses the full alignment context (as opposed to the filtered one)
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-MQ0 annotation is now standard again
-Added AC and AN annotations to VCF output
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2545 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-08 05:40:42 +00:00
f587ff46af
Tile is now a standard covariate. By default the TileCovariate returns -1 if tile can't be derived from the read's name. Added a new command line option -throwTileException which will force TileCovariate to throw an exception if tile can't be derived for a read. Singleton covariates, such as any read group without tile info, must be skipped over in TableRecalibration so that the sequential formulation doesn't apply the same correction more than once. TileCovariate class has been added to the Early Access package.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2544 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-07 22:51:41 +00:00
d01bde36a4
Make sure that reference view holds enough bases to pass full-length deleted sequence to the walker's map() function in extended event mode (this addresses the problem of a deletion crossing the shard's boundary, so that an attempt to extract deleted bases results in a crash)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2543 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-07 22:37:22 +00:00
e9bc85c188
Now has methods that allow to 1) check if a location is within the bounds of the reference view; 2) expand reference view (i.e. expand the bounds and reload the reference sequence) in order to accomodate specified location. The second method can be called directly since it performs a check and if the location is already within the bounds, then returns immediately. The costly ref sequence reloading occurs only when the location is not fully contained within the current bounds.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2542 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-07 22:35:17 +00:00
7f91b4d824
Bug fix. It would be nice if we could extract ROD annotations for the whole length of an extended event (indel), and we tried... But alas, it does not work with the current ROD system (after extracting length on ref > 1 ROD data for a deletion, rod iterator crashes on the attempt to re-load annotations for next reference base)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2541 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-07 21:30:55 +00:00
5f58492401
A rogue QualityUtils.MAX_REASONABLE_Q_SCORE managed to get through my previous bug fix. It should instead check the command line -maxQ argument.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2540 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-07 21:17:39 +00:00
c7a8dffa89
Check for division by 0 in annotations
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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
9a658e6b18
-Fixed VCF header line bug
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-Added useful trim() method for Strings for characters other than whitespace
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2538 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-07 17:51:41 +00:00
b643a513bb
Minor interface change for VCFGenotypeRecord.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2537 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-07 16:48:09 +00:00
431e9c2c8b
Add dbSNP ID to VCF output records
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2536 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-07 15:30:04 +00:00
076481f786
Fixes to mergeVCF -- now correctly supports merging of filter fields. Also removed incorrect hasFilteringCodes() function. Updated intergration tests
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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
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.
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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
6c739e30e0
1. Removing an old version of the Genotype interface which is no longer being used. Needed to do this now so that the naming conflicts would cease.
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2. Adding a preliminary version of the new Genotype/Allele interface (putting it into refdata/ as the VariantContext really only applies to rods) with updates to VariantContext. This is by no means complete - further updates coming tomorrow.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2533 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-07 05:51:10 +00:00
a9245a58e2
Fix for incorrect exception throwing in VCFRecord. It is reasonable to ask for the non-ref allele freq at all ref sites. Was only passing in tests because isReference was broken
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2532 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-07 01:18:30 +00:00
7215526810
Fix to isReference() in VCFRecord. Change to VariantCounter to correctly counter only non-genotype variants, as well as update to VariantEvalWalker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2531 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-07 00:03:29 +00:00
6c4ac9e663
Updated HapMap2VCF to use the VCFGenotypeWriterAdapter interface; fixed bug in VCFParameters that affects VariantsToVCF and HapMap2VCF when reference is lower-cased; added integration test for HapMap2VCF that checks for the lower-case issue by testing against Hg18 region that has lower-cased bases
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2530 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-06 21:27:11 +00:00
576594eda2
clean-up of the GATK paper genotyper, and better output formatting for the simple call format we emit.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2529 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-06 20:54:56 +00:00
7e3e714d3c
Moving experimental annotations from core to oneoffs
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2528 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-06 19:34:10 +00:00
a32245f7d2
Modifications:
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QualityUtils - Stole the BaseUtils code for flipping reads around and applied it to quality scores
SecondBaseSkew - Nothing's really different, just a commented line
Additions (experimental annotations for future development of second-base annotation)
** I DO NOT INTEND FOR ANYONE TO USE THESE **
- ProportionOfNonrefBasesSupportingSNP
- ProportionOfSNPSecondBasesSupportingRef
- ProportionOfRefSecondBasesSupportingSNP
+ I hope these are self-explanatory
- QualityAdjustedSecondBaseLod
+ Adjust lod-score by 10*log10[P[second bases are as observed]]
Added walker:
QualityScoreByStrand - oneoff project that's being saved if i ever need it
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2527 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-06 19:18:07 +00:00
eb899741e1
reverting last changes. no cacheing
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2526 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-06 18:59:37 +00:00
a17d725c35
Cache pileup bases and mapping quals after first call to getBases() and getMappingQuals(), respectively. Subsequent calls to these method will return cached arrays.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2525 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-06 18:05:00 +00:00
d6fb19bb67
Don't hard-code base qual max
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2524 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-06 17:21:44 +00:00
75809100c6
Use inheritance so that shared code isn't duplicated between the RecalDatums
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2523 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-06 16:45:16 +00:00
fdd14e1a01
Proposed interface for VariantContext. It's currently an interface so it doesn't break the build...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2521 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-06 16:31:39 +00:00
e011a1b6f8
Cut the memory footprint of the RecalDatum in half to improve performance of CountCovariates when run with many covariates.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2520 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-06 16:12:27 +00:00
370a365147
Small runtime improvement in TableRecalibration.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2519 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-06 15:51:12 +00:00
b745c2f8d7
Fix for Jared: don't blow up if there are no samples in the input (since that's allowed) - but warn the user just in case.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2518 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-06 15:37:06 +00:00
1e462419da
trivial code restructuing, and commented out failed attempt to support sample selection with VCF. VariantEval2 go go go
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2516 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-06 15:04:27 +00:00
f857159343
useful convenience function to get a genotype associated with a particular sample
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2515 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-06 15:03:07 +00:00
34519b3e3b
Better printing support for false positives and false negatives in concordance tables
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2514 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-06 15:02:40 +00:00
592749a7c1
isNBase method
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2513 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-06 15:01:51 +00:00
5ce11c3dad
toString method
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2512 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-06 15:01:20 +00:00
1c90e6a954
More informative error message in AnalyzeCovariates and cleanup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2511 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-06 14:56:29 +00:00
bca3d1b943
useful convenience function to get a genotype associated with a particular sample
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2510 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-06 14:53:56 +00:00
ec774f62be
Some checking to protect the BasicGenotype
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2509 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-06 14:53:24 +00:00
71ecbe75d7
AnalyzeCovariates would crash with 'too many open files' exception when spawning Rscript jobs for every read group at once. It now waits for some to finish before spawning the rest.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2508 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-06 14:19:02 +00:00
21a50eedb5
Simple extension to VariantEval: --includeFilteredRecords will now keep filtered VCF records so you can see what the entire call set looks like. Looking forward to VariantEval v2 from Kiran.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2506 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-06 12:59:09 +00:00
8d13597a27
Temporary command-line support to enable rod walkers, if you know what you are doing this is safe.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2505 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-06 12:15:36 +00:00
d8351cb9fc
Give Annotations access to rod data.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2504 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-05 18:53:01 +00:00
8b087305f3
Added back the MQ0 annotation - however, it's not yet standard (since mq0 reads are filtered out by default in the genotyper). But it'll work when using the Annotator as a standalone.
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While I'm at it, change getPileup to getBasePileup to remove all of the deprecation warnings.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2502 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-05 17:07:19 +00:00
a4b69d0adf
Misc bug fixes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2501 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-05 14:48:19 +00:00
c209ba55aa
More informative error message
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2499 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-05 13:55:20 +00:00
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.
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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
ed2fff13aa
-Misc improvements to VCF code
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-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
29c129aced
Added very primitive read fishing walker with lots of hard coding. Fixed
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bugs encountered when testing read fishing in Ecoli.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2496 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-04 00:54:57 +00:00
7b702b086f
You don't need to be bi-allelic to have a non-ref alt allele frequnecy, but you do have to be a variant.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2495 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-03 22:02:39 +00:00
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.
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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
b6ecc9e151
Support for ad-hoc reference sequences. Also reenabled BWA/Java integration test, which was commented out
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and the data backing it up deleted without my knowledge. Unfortunately, since the data was deleted, I had
to regenerate the data and a new md5. Hopefully the aligner output is still correct.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2493 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-02 20:19:14 +00:00
ad549eacfd
Now that we changed how deletions are represented, got to update MD5...
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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
46362ce532
In extended event lines, now prints deletions in verbose format as well (e.g. "-AAT")
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2490 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-30 21:57:20 +00:00
a18e31f5b8
If alignment context at the locus holds extended event, get rod metadata and (importantly) reference bases for the whole span of the event (if it is a deletion that is, insertions still have length 0 on the ref!)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2489 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-30 21:56:25 +00:00
a41cb0701b
Now can generate verbose String representation of deletions (e.g. "-AAT") if reference bases are provided as an argument to getEventStringWithCounts().
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2488 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-30 21:54:50 +00:00
89791d730e
Compute and cache the length of the longest deletion observed at the site; ReadBackedExtendedEventPileup now has a getter to access that value.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2487 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-30 21:19:39 +00:00
9c41ac252f
Disable testSingleBPFailure - getReferenceContext() now whould agree to accept length > 1 genome locs as its argument, so there's nothing to test...
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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
8932e67325
Removed sanity check that required GenomeLoc argument to be strictly 1-base long. We need to relax this in order to be able to pass around a reference context containing full-length chunk of deleted reference bases
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2485 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-30 20:14:08 +00:00
497ae700c4
A rethink of the existing BAM block extraction code: rather than working in
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chunk space directly, stream data in block space, converting to chunk space
on demand.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2484 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-30 18:19:51 +00:00
80658fd99e
AnalyzeCovariates gets the same performance improvements as the recalibrator. NHashMap class is removed completely.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2483 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-30 18:10:10 +00:00
9b2733a54a
Misc clean up in the recalibrator related to the nested hash map implementation. CountCovariates no longer creates the full flattened set of keys and iterates over them. The output csv file is in sorted order by default now but there is a new option -unsorted which can be used to save a little bit of run time.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2482 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-30 16:58:04 +00:00
4aeb50c87d
Added: integration test for extended pileup (with indels included)
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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
c928347c0c
Extended event pileups are more verbose now: following a sequence of 'D','I', and '.' symbols, actual distinct events are listed along with their counts (example: +AAA:3,+AAC:1 for the total of 4 indel observations with 3 reads showing +AAA and one read showing +AAC)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2480 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-29 22:44:18 +00:00
8330058216
method added: getEventStringsWithCounts()
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Returns list of Pairs <String,Integer>, where each pair consists of a unique indel event observed at the site and the total number of observations of that event. String representation for insertions is verbose (e.g. +ACT), while deletions are represented as "5D" (since read backed pileup has no reference information, so we can not get actual sequence of deleted bases)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2479 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-29 22:41:58 +00:00
cf3e59eb4a
back to archive
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2478 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-29 22:00:38 +00:00
295d16572e
synch; will go back to archive in a sec
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2477 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-29 22:00:03 +00:00
e286313b67
Fix for reads that have insertion as their last (mapped) cigar elements (i.e. not followed by M)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2476 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-29 21:13:16 +00:00
05deb8796b
Simplify handling of reference sequence for unmapped reads. Improvement made based on a suggestion from Alec.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2475 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-29 21:06:20 +00:00
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.
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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
7826e144a1
forgot to update md5s
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2473 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-29 20:31:29 +00:00
bfd6bf9ec5
PileupWalker just got a new option: --showIndelPileups. When this option is used, two lines are printed for every genomic location that has indels associated with it: first line is a conventional base pileup, the second line is an "extended event" (indel) pileup. The refence base in that second line is always set to "E" (for Extended), and the pileup string contains I,D,. symbols for insertion, deletion, noevent, respectively. Only this simple short format for indel pileups is implemented so far.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2472 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-29 20:16:34 +00:00
9652692019
Modified to enable locus traversals firing additional calls to walker's map() with alignment context filled with extended events (indels). Walker should override generateExtendedEvents() to return true, and it should make sure that it catches those additional indel pileups and processes them differently, as needed. If there are indels associated with a specific reference base, TWO map() calls will be issued in locus traversal at that location: first one will have a context filled with a regular base pileup, the second call will provide the context filled with indel pileup (pileup elements will have insertion, deletion, or noevent type associated with them and will also carry information about the full length of the event and inserted bases).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2471 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-29 20:13:25 +00:00
06eb576924
Can now be constructed with either base pileup or extended event (indel) pileup; has query methods checking what kind of pileup is served by the context, and getter methods return the appropriate pileup. TODO: while it is impossible right now to create a context that contains both types of pileups simultaneously, this restriction is only weakly enforced through the lack of appropriate constructor. Either we keep it this way, or some getters may become ambiguous and have to be fixed!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2470 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-29 20:07:29 +00:00
f445745c56
Pileup element and corresponding container class tweaked for representing pileups of extended events (indels) at a given locus. There's some redundancy with PileupElement and ReadBackedPileup (should we rename them to BasePileupElement and ReadBackedBasePileup?), so that abstracting a basic interface/abstract base from these classes can be considered in the future
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2469 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-29 20:03:39 +00:00
87e863b48d
Removed used routines in duputils; duplicatequals to archive; docs for new duplicate traversal code; general code cleanup; bug fixes for combineduplicates; integration tests for combine duplicates walker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2468 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-29 19:46:29 +00:00
29f94119d1
Fixes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2466 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-29 18:08:41 +00:00
5fdf17fccb
Removed the VCF "NS" annotation (which wasn't working for pooled calls anyways) since it's ambiguous and not useful.
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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
e32174fbc4
UnifiedGenotyper now works without -varout or -vf set.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2464 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-29 16:46:24 +00:00
b125571a98
Intermediate check in: transfer responsibility of wrapping the GenotypeWriter around the output stream to the output
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management code. Currently, will not work when neither -varout nor -vf are specified, but should work in all other
cases.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2463 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-29 16:11:11 +00:00
aeb34758e6
Adding a validation stringency to the VCF writers (which defaults to STRICT). If set to SILENT, it will not throw an exception for (reasonable) off-spec requests but will instead ignore such requests and silently move on.
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This change allows the pooled calculation model to work correctly with multiple threads. Boys, the Genotyper is now officially parallelized.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2462 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-29 15:33:53 +00:00
29a3d9b47a
AnalyzeCovariates also has to skip over NO_DINUC
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2461 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-29 14:36:05 +00:00
a34c2442c0
moved hard-coded file paths to the oneKGLocation, validationDataLocation, and seqLocation variables setup in the BaseTest.
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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
9d263b2565
Integration tests for count duplicates walker validated on a TCGA hybrid capture lane.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2459 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-28 23:57:25 +00:00
fcc80e8632
Completely rewritten duplicate traversal, more free of bugs, with integration tests for count duplicates walker validated on a TCGA hybrid capture lane.
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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
4617052b3c
For Alec, and others at the Broad who want to run our unit/integration tests off of gsa1/gsa2: put a ceiling on the amount of memory that integration tests can use. Reduce the memory footprint of the fasta reader test.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2457 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-28 23:42:46 +00:00
b5e5e27225
New versions of picard-private, sam and picard jars for TileCovariate and regeneration of NM tag
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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
d4ee999ef9
Creates files supplemental to the reference sequence, consumed by BWA.
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ANN - Alternate form of the sequence dictionary. Should be created from a sequence dictionary with full contig names.
AMB - A map of 'holes' in the genome, aka runs of non-ACGTacgt bases. This skeletal implementation always reports no
holes.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2455 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-28 21:40:44 +00:00
fcc52fbcd1
Fixed the build. Added missing import line.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2454 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-28 21:26:00 +00:00
893c9c85fa
Added previous optimization to diploid (non-pool) model and shaved off 20% of runtime from it. Moved out some common functionality to joint estimate parent class.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2453 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-28 21:20:48 +00:00
92e3682991
Moved NHashMap to sting/utils
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2452 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-28 20:57:32 +00:00
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.
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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
2a704e83df
Reads now have new traversal flag: generateExtendedEvents(). Support added to GenomeAnalysisEngine and Walker. This is a silent and transparent framework change that no existing code is going to see. The actual code that makes use of the new flag (which is false by default) will be committed separately...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2450 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-28 19:52:44 +00:00
c8d0e6e004
Optimization to pooled calculation model: stop calculating P(D|AF) if we are beyond the max likelihood such that subsequent likelihoods won't factor into the confidence score. Also, use new Pileup interface.
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Pooled calling now takes less than half the time it used to.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2449 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-28 18:39:55 +00:00
b1ac4b81d5
Optimization: look up diploid genotypes from a static matrix instead of creating them on the fly (with String.format); bases no longer need to be ordered appropriately
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2448 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-28 17:28:51 +00:00
57516582c2
Converter from HapMap chip genotype data to VCF added; HapMapGenotypeROD adjusted to not convert from Hg18 to b36 formatting of contigs
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2447 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-28 01:36:08 +00:00
d2770f380c
Writing calls to standard out now works again (it got broken when we introduced parallelization)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2446 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-27 04:36:45 +00:00
12990c5e7a
Added qual-by-depth annotation
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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
hanna
rpoplin
asivache
andrewk
depristo
aaron
chartl
alecw