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
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
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
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
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
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
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
0571d9dcb9
Point MAX_QUAL_SCORE to SAMUtils.MAX_PHRED_SCORE.
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Also, array size for caches should be max score + 1.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2444 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-24 20:47:32 +00:00
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.
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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
aaf674d9db
Cleaned up this annotation.
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Still experimental. As of now, it's not useful. More analysis is needed to determine how to handle cases where UG is unsure whether a sample is het or hom.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2442 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-24 03:06:46 +00:00
6df40876a3
Un-reverted Matt's previous changes and fixed integration tests.
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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
2bd0b1bbf7
After further review, it's unclear that my patch in RecalDataManager was the right choice. Reverting.
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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
98c268483e
Fixed issues with the integration tests:
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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
b134e0052f
added changes to the code to allow different types of interval merging,
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1: all overlapping and abutting intervals merged (ALL),
2: just overlapping, not abutting intervals (OVERLAPPING_ONLY),
3: no merging (NONE). This option is not currently allowed, it will throw an exception. Once we're more certain that unmerged lists are going to work in all cases in the GATK, we'll enable that.
The command line option is --interval_merging or -im
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2437 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-23 21:59:14 +00:00
159778416c
In TableRecalibrationWalker, update UQ tag if it was present in the original SAMRecord. This required a new sam.jar, which caused some other files to need to be changed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2435 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-23 21:42:36 +00:00
87ff2b15d4
First step in introducing a patch to Picard: create our ideal interface into the BAM file for sharding.
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This commit can iterate over the BAM file, pulling out information about the blocks in the file without actually loading
or decompressing the reads.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2434 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-23 21:35:08 +00:00
dc96879861
2 separate changes which both affect lots of UG integration md5s, so I'm committing them together:
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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
872a9d1c7b
I'm making this change now (as opposed to waiting until Monday) to honor Tim's request.
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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
e29e8e52b9
Multithreading support for the unified genotyper. Tests on a 10Mbase region on pilot 1 show a 6.8x improvement
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when running 8 ways parallel.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2430 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-23 00:48:06 +00:00
164a94a3d0
Modified the walker documentation so that the stray punctuation wouldn't cause the GATK to stop parsing the help documenation early (aka I changed one word).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2429 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-22 20:50:01 +00:00
4ee6a478e3
Creates a table of reference allele percentage and alternate allele percentage at Hapmap-chip sites in a BAM file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2428 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-22 20:43:44 +00:00
03bf75e335
Now implements TreeReducible
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2427 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-22 17:52:51 +00:00
0d890e1bf0
Rework Eric's output management code given that the behavior of the UG changes drastically
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depending on its output format. Current implementation is probably a bit overkill-ish and
we can whittle this down to what's absolutely necessary.
Writing VCFs to the 'out' protected printstream may not work at this moment.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2425 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-22 00:33:43 +00:00
f448a263e9
The cleaner now cleans duplicate reads (instead of ignoring them) - although it doesn't include them for scoring ref or alt consenses
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2424 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-21 21:01:55 +00:00
cf303810d3
VCF reader now creates the correct type of header line for each header type
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2423 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-21 20:39:06 +00:00
e06dfe44c4
Check for null platform (even when the read group isn't null) and assign it the default platform if it is
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2420 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-21 07:01:41 +00:00
87e5a41964
Fixed a bug that accounted for a bunch of my remaining mis-cleaned indels.
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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
b780ffb34a
Add a getFormat() method to get the output format from the writer. The need for
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this call suggests that I may be thinking about the typing of the GenotypeWriter object the wrong way.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2418 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-21 01:46:26 +00:00
11cbfcec9c
Get rid of backlink from ArgumentDefinitions to ArgumentSources. This will help in the future with multiple
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source -> single definition mapping sets.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2417 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-21 00:39:36 +00:00
9e53c06328
First revision of command-line argument support for GenotypeWriter. Also, fixed the damn build.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2416 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-20 19:19:23 +00:00
4ff61097cf
Trivial change: < -> <=
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2415 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-20 03:35:27 +00:00
566b556b50
Give user ability to turn off max allowed interval size
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2414 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-20 03:20:22 +00:00
a5f75cbfd4
The previous commit broke the build, so this is a temporary patch to get it to compile. ConcordanceTruthTable should use enums (esp. now that all of the concordance variables need to be public), but VariantEval will need to be rewritten soon anyways so I'll just push it off until then.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2413 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-20 02:34:41 +00:00
ee8bcdc61d
PooledConcordance calculations have been reformatted and bugs fixed. Now properly handles monomorphic sites. Also works with -G option now, correctly
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2412 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-19 23:22:36 +00:00
9bf2d12c64
Misc. improvements to the LMW code. Support for emitting all sites, regardless of genotype. Min and max quality scores.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2411 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-19 23:20:57 +00:00
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.
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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
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.
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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
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.
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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
c39675d2c1
VCFTool.java got left off of the last commit
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2407 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-18 21:33:53 +00:00
4ea31fd949
Pushed header initialization out of the GenotypeWriter constructors and into a writeHeader method, in preparation for parallelization.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2406 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-18 19:16:41 +00:00
eeddf0d08e
Adding sample utils for convenience methods to pull out samples from e.g. SAMFileHeader or Genotype objects
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2405 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-18 18:51:21 +00:00
79b997f43d
Minor fix to getValue (thanks Ryan!)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2404 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-18 15:45:51 +00:00
9971a8da9a
adding a check to the RodVCF to ensure that records are in-order in the underlying VCF file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2403 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-18 15:24:45 +00:00
38563bbc2d
The values used to be integers (-1 for unpaired, 0 for unmapped, 1 for first, 2 for second); but i switched to strings before commit so it was more clear. Forgot to update the OTHER getValue method.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2402 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-18 15:05:14 +00:00
7b5e332ff3
Added - PairedQualityScoreCountsWalker: counts quality scores (e.g. as a histogram) on first reads of a pair and second reads of a pair. Turns out there's a consistent difference in quality scores; even after recalibrating without the pair ordering as a covariate (there's a bit of averaging -- but not as much as I initially thought).
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Added - A paired read order covariate to use with recalibration. Currently experimental: for instance, what's a proper pair versus just a pair? Nobody should use this one...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2401 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-18 15:01:01 +00:00
4f59bfd513
Updates to the various GenotypeWriters to make them do simple things like write records (plus allow GLFReader to close).
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Adding first pass of stub and storage classes for the GenotypeWriters so that UG can be parallelizable. Not hooked up yet, so UG is unchanged.
The mergeInto() code in the storage class is ugly, but it's all Tribble's fault. We can clean it up later if this whole thing works.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2400 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-18 07:20:23 +00:00
94f5edb68a
1. Fixed VCFGenotypeRecord bug (it needs to emit fields in the order specified by the GenotypeFormatString)
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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
98839193b7
compatibility with VCF lib's switch to GenomeLoc.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2397 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-18 00:52:48 +00:00
8787dd4c5e
Various and sundry additions to VCF tools. Some useful to the general public, some one-offs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2396 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-18 00:35:45 +00:00
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.
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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
c75ec67f84
When called as a standalone, VariantAnnotator now emits samples in sorted (as opposed to random) order in VCFs.
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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
aa86f3710d
Updating HomopolymerCovariate to only count the consecutive previous bases. I left in the code but commented out for if somebody wants to worry about carry forward homopolymer problems.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2391 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-17 18:25:09 +00:00
9143822822
Fix half-hearted attempt to try to move classes from package to package.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2389 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-17 17:41:42 +00:00
acb4d477da
sync...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2387 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-17 01:03:01 +00:00
ba86508854
remove debug print command
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2386 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-17 00:00:01 +00:00
d72d332239
1) changed to search specifically for D and I cigar elements (and to process properly/ignore H,S,P elements) and print out only intervals that encompass actual indels. There's still one interval per read (at most) generated, which is the smallest intervals that covers ALL indels (D or I elements) present in the read; 2) if an interval (thus the original read itself and indels in it) sticks beyond the end of the chromosome, the read is ignored and this interval is NOT printed into the output; instead, a warning is printed to STDOUT (should we send it to logger.warn() instead?
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2385 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-16 23:29:07 +00:00
5b78354efd
Fixed NPE in index check with RefWalkers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2384 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-16 22:37:45 +00:00
e6127cd6c5
Temporary hack for Tim Fennell: introduce a sharding strategy that stuffs all data into a single
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shard for cases when the index file isn't available. Works for the case in question, but is not
guaranteed to work in general. Will be replaced once the new sharding system comes online.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2383 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-16 21:55:42 +00:00
bef1c50b3b
Some cleanup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2382 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-16 21:41:06 +00:00
bb92e31118
Optimizations:
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1. push the ReadBackedPileup filtering up into the ReadFilters for read-based filters
2. stop querying the cigar for its length (just do it once)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2381 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-16 21:39:58 +00:00
36875fca89
Update documentation in the new help system
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2380 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-16 21:33:12 +00:00
ee47eb4367
Make filters used available to the walker via getToolkit().
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2379 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-16 21:26:04 +00:00
b626fc0684
Joint Estimate is now the default calculation model.
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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
e051311e8c
Added convenience methods in RodVCF to pull out all of the VCF data from the VCFRecord (e.g. getID(), getSamples(), getInfoValues())
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2374 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-16 17:58:41 +00:00
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).
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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
af440943a4
Fixing a bug that Steven uncovered; we had an abigous contract for peek() in PushbackIterator, and SeekableRODIterator wasn't checking to see if it's PushbackIterator hasNext() was true before calling peek().
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Changed peek() to element() to be consistant with the Java standards of the Queue and Stack classes (element() throws an exception if a record isn't available).
Also updated some of the ROD iterator next() methods to throw NoSuchElementException if next() is called when a record isn't available.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2372 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 23:04:40 +00:00
1035abc85f
Add minimum base quality thresholding to depth of coverage via getBaseAndMappingFilteredPileup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2371 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 22:58:30 +00:00
2deae95df9
Updated documentation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2370 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 21:31:47 +00:00
555976d575
One more walker with formatting to fix.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2369 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 21:23:13 +00:00
cf46472419
Fix up Sherman's new docs in compliance with javadoc specs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2368 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 21:20:38 +00:00
df79ed8db1
Updated documentation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2367 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 20:53:41 +00:00
a80a5f1036
Updated documentation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2366 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 20:52:08 +00:00
18f61d2586
Updated documentation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2365 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 20:45:19 +00:00
5974c42468
Updated documentation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2364 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 20:41:35 +00:00
d8cfd707bc
Updated documentation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2363 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 20:35:18 +00:00
4322beeb35
Updated documentation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2362 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 20:33:38 +00:00
4148991d81
Now also encodes amino acids, includes documentation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2361 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 20:26:56 +00:00
9b0bdbbf29
Fix for homopolymer bug: ref was lowercase, alt allele was uppercase, so alt != ref. Yuck.
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This is a temporary fix - pushed more elegant solution over to Matt.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2360 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 19:02:23 +00:00
a810586418
Check-in without javadoc = smackdown
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2359 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 15:32:39 +00:00
b234019cf5
Readded locus printing suppression to DoC walker
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(and removed unused import from UG)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2358 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 14:50:56 +00:00
0d2a761460
Bugfix for minBaseQuality to ignore deletion reads. LocusMismatch walker now allows us to skip every nths eligable site
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2357 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 14:38:39 +00:00
bf7bab754e
Made getPileupWithoutMappingQualityZeroReads() and getPileupWithoutDeletions() more efficient, per Mark's cue.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2356 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 04:35:21 +00:00
874552ff75
Pull the genotype (and genotype quality) calculation out of the VCF code and into the Genotyper.
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[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
2cbc85cc7a
min mapping quality and min base quality arguments for UG
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2354 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 03:57:27 +00:00
faa638532a
Correct location
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2353 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 02:42:21 +00:00
1da97ebb85
Walker for calculating non-independent base errors, v1. Will be moved to somewhere not in core
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2352 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 02:40:15 +00:00
b42fc905e8
Added - new tests (Hapmap was re-added)
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Modified - Hapmap now takes a -q command to filter out variants by quality
Modified - MathUtils - cumBinomialProbLog now uses BigDecimal to handle some numerical imprecisions
Modified - PowerBelowFrequency - returns 0.0 if called with a negative number (can't be done from inside the walker itself, but since it's called elsewhere one can't be too careful)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2350 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-14 21:57:20 +00:00
8e44bfd2ef
CycleCovariate and PrimerRoundCovariate now correctly handle negative strand 454 and SOLID reads.
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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
c7b23d6ca5
Now that VCFGenotypeRecords implement SampleBacked (as they should), a quick fix was needed to get the GenotypeConcordance working when no direct samples were provided in a samples file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2348 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-14 04:27:16 +00:00
bd7b07f3f1
added PrimitivePair.Long and a few shortcut utility methods to PrimitivePairs: add(pair), subtract(pair), assignFrom(pair)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2347 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-14 00:15:44 +00:00
97618663ef
Refactored and generalized the VCF header info code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2346 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-13 21:02:45 +00:00
05b8782d5f
Documentation updates. Moved CountX.java walkers to QC
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2345 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-13 18:40:22 +00:00
92307361a4
In preparation for move
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2344 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-13 18:28:06 +00:00
45199136f0
Completed my documentation responsibilities - based on Mark's reasonable assignment and not the one Matt made up while on Meth.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2342 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-13 04:13:30 +00:00
bd2a46ab4c
I want to move over to hpprojects tonight, so I'm checking in various changes all in one go:
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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
2748eb60e1
Added short documentation for each class so that it appears in the walker command-line documentation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2340 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-12 21:41:07 +00:00
78e94b5a84
TableRecalibration now puts the full list of walker arguments into the PG tag of the bam file it creates. Thanks Matt and Eric. Also, the default nback for the HomopolymerCovariate is 8, down from 10.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2339 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-12 17:29:41 +00:00
014013630f
Added hieracrchy to the covariate classes: Required, Standard, and Experimental. Required covariates (rg and reported quality) are added for the user whether or not they are specified in the -cov list. There is now a -standard option in CountCovariates which will add in all of the standard covariates so the user doesn't have to type them all out or even know which ones are the standard. There is logger output to say which covariates are being used of course. The list of covariates used is also added to the PG tag in the bam file produced by TableRecalibration.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2338 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-12 16:34:05 +00:00
6955b5bf53
Cleanup of the doc system, and introduce Kiran's concept of a detailed summary
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below the specific command-line arguments for the walker. Also introduced
@help.summary to override summary descriptions if required.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2337 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-12 04:04:37 +00:00
cdfe204d19
Incorporated feedback from Kiran. Use the Javadoc first sentence extraction capability to just show the first sentence from each line of Javadoc. @help.description can still be used to produce exceptionally verbose descriptions.
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Also increased the line width as much as I could tolerate (100 characters -> 120 characters).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2336 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 21:59:55 +00:00
4fa4e95fbc
Updated AnalyzeCovariates to extend org.broadinstitute.sting.utils.cmdLine.CommandLineProgram and use the standard argument parsing.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2335 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 21:57:18 +00:00
38d9f7b903
Renamed ReferenceContext's getSimpleBase() method to getBaseIndex()
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2334 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 20:14:39 +00:00
09811b9f34
Now that we always output the VCF header, make sure that we correctly handle the situation where there are no records in the file. Added unit tests as well.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2333 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 19:51:05 +00:00
0da2105e3c
Moving DuplicateQualsWalker to oneoffprojects.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2332 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 19:22:32 +00:00
60c3eb4b60
Added help.description to the recalibration walkers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2331 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 19:02:29 +00:00
2ea7632b76
The SNP genotype concordance module is now more comprehensive.
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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
590aeee7d2
Documentation for more basic walkers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2329 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 18:15:40 +00:00
d1815f3559
More documentation for walkers that I'm familiar with in the collection of core walkers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2328 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 18:02:33 +00:00
956c36a2c8
Help for the qc package.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2327 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 17:32:47 +00:00
450ea233a5
Docs for the basic walkers: CountLoci, CountReads.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2326 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 17:17:34 +00:00
f97ac939fa
Punch up the help documentation for CombineDuplicates.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2325 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 17:09:35 +00:00
86dc98bfb5
update the documentation for CombineDuplicates for the new help system.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2324 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 17:01:42 +00:00
420725441a
documentation updates for the new help system.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2323 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 16:15:44 +00:00
23d96b1d43
Help system content for the alignment module.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2322 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 16:01:25 +00:00
2de7e1a178
Move VariantAnnotator over to use a StratifiedAlignmentContext split by sample.
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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
8f7554d44f
A few improvements to pooled concordance calcluations. Now will show you FN with the -V option. BasicGenotype now prints out a reasonable representaiton wiwth toString
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2320 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-10 23:09:10 +00:00
f64a4c66ac
some tweaks for the GATK paper genotyper to better work with shared memory parallelization, added documentation changes for Matt's new help system.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2319 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-10 22:33:51 +00:00
a7cd172628
Added 8x coverage field and minimum base quality command line option in order to be able to compare to U. Wash. exome metrics.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2318 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-10 22:14:44 +00:00
2869270c11
Fixed deletion depth calculation plus mis-spelling in ReadBackedPileup method.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2315 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-10 21:11:42 +00:00
31b1d60d28
Generalized the StratifiedAlignmentContext code so that it's easy to add new ways to stratify. Then added an MQ0-free stratification so we don't need to be carrying around 2 different alignment contexts (full vs. mq0-free) anymore.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2314 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-10 19:50:06 +00:00
0c396f04a2
Fix obvious cut/paste error in output stream management code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2313 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-10 19:23:13 +00:00
11ac7885b0
Pull out StratifiedAlignmentContext code so other walkers can use it.
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This is basically a wrapper class around AlignmentContext which allows you to stratify a context by e.g. reads on forward vs. reverse strands.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2312 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-10 19:21:16 +00:00
adb2fdbee7
Before, we were only checking that the reference was present if @Requires required that a reference was present. Now we always check that a reference is present, so that we get an intelligent error message.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2311 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-10 19:15:48 +00:00
5eac510b2f
Refactor the code I gave Eric yesterday to output command line arguments.
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Convert it from a completely wonky solution to a slightly less wonky solution
that will work in more cases.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2310 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-10 18:57:54 +00:00
74b8055b6a
Only show extra walker help if the user didn't specify a walker or specified
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an invalid walker.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2309 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-10 16:43:06 +00:00
0fae798b3a
1. Discoverable base calculations don't care about Genotypes (use Variation's PError regardless of whether the call is ref or var - it's the correct value even for ref calls).
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2. Call a base genotypable if any of the Genotypes is above the threshold (you can't assume there's a single Genotype associated with the Variation).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2306 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-10 04:26:06 +00:00
a45adadf1f
VCFGenotypeRecord already defines all the methods needed to be SampleBacked, so let's annotate it as being SampleBacked. This way, when used as a generic Genotype, sample data can be retrieved.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2305 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-10 04:16:21 +00:00
78d5ac9bc2
Don't check het count when there are multiple Genotypes per Variation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2304 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-10 04:07:47 +00:00
f7c44ad019
- Read in arguments for the header based on reflection
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- 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
408f6f3dee
Refactoring of prior commit: better handling of unnamed package within the help system.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2297 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-09 20:12:35 +00:00
1d2151adcf
Better handling of nulls output by
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2296 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-09 19:34:56 +00:00
40c2d7a4bc
Fix all-bases-mode and genotype-mode in the UG and add integration tests for them.
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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
4e54b91ce4
UG now outputs the FORMAT header fields when there's genotype data.
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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
12c49ea485
Added DuplicateReadFilter to filter out reads that are marked as duplicates.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2293 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-09 15:42:53 +00:00
fb900b12e1
VariantFiltration now details the filters it has used in the header of the VCF it produces.
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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
7a76e13459
Better explanation in the exception being thrown.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2291 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-09 03:59:36 +00:00
8d67d9ade3
-Minor fix in UG for all-bases mode
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-Make minConfidenceScore in VariantEval a double so non-integer values can be used (requested by Steve H).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2290 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-09 03:49:10 +00:00
717eb1de96
- Depth annotation now includes MQ0 reads
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- 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
e8822a3fb4
Stage 3 of Variation refactoring:
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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
9e2f831206
A bit of cleanup in preparation for Picard patch.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2286 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-08 16:09:04 +00:00
d3b78338da
Get rid of characters in the docs that aren't universally compatible with
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character sets used throughout the group.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2285 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-07 21:41:07 +00:00
d75d3a361a
Clean up some of the walker help output based on additional experience and
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feedback received. Also, add a flag to build.xml to disable generation of
docs on demand (use ant -Ddisable.doc=true to disable docs).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2284 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-07 21:33:11 +00:00
a3e88c0b1c
Cleanup results of bad merge.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2281 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-07 19:30:49 +00:00
10be5a5de9
Move some files around to reflect our growing help infrastructure.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2280 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-07 19:23:12 +00:00
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.
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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
8f461d3c40
Critical bug fix for VariantEval dbSNP calculations. Moved the system over to the new improved ROD iterators, resulting in dbSNP rates jumping 5% or so, due to masking of true SNPs by preceding indels.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2274 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-07 03:36:38 +00:00
8089aa3c50
Adding support to override the help text.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2273 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-07 00:16:26 +00:00
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.
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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
b6f8e33f4c
Stage 2 of Variation refactoring:
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VCFRecord now implements Variation, VCFGenotypeRecord now implements Genotype.
Because of this change, RodVCF is now just a wrapper around the VCFRecord and does nothing else. Also, one can call toVariation on the VCFGenotypeRecord and it returns the VCFRecord.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2271 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-06 06:48:03 +00:00
3b440e0dbc
Add a taglet to allow users to override the display name in command-line help.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2270 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-06 04:12:10 +00:00
08f2214f14
Stage 1 of massive Variation/Genotype refactoring.
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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
b04de77952
First pass at a reorganized walker info display. Groups walkers by package
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and displays walker data extracted from the JavaDoc. Needs a bit of help,
both in content and flexibility of package naming.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2267 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-04 23:24:29 +00:00
07b88621c5
Improved RankSum calculations and RankSum annotation. Much more meaningful
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2266 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-04 22:16:40 +00:00
4c147329a9
Turn javadoc comments for packages and classes into key/value pairs in a properties file. Embed the properties file
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in GenomeAnalysisTK.jar. Still no support for actually displaying the archived javadoc. Also change the approach
to providing package javadocs: retired the deprecated package.html file in favor of Java1.5-style package-info.java.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2263 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-04 20:08:41 +00:00
1e8dcc30da
-dbSNP rod should not implement VariantBackedByGenotype since dbsnp records have no genotype data
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-added code to cache the allele list so it didn't need to get recomputed each time it was requested.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2260 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-04 14:56:48 +00:00
58937bf9ba
You can now use the -exp flag to tell the Genotyper to include experimental annotations when it calls out to VariantAnnotator.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2256 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-04 04:45:05 +00:00
b05e73a914
Finished implementation of the Wilcoxon Rank Sum Test thanks to Tim Fennell (calculating the normal approximation) and Nick Patterson (dithering to break tie bands).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2255 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-04 04:04:39 +00:00
861221d046
- Moved various header line printing into a single method
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- 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
aef4be5610
Moved CoarseCoverageWalker to core and packaged both coverage walkers in coverage/
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2249 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-03 17:53:36 +00:00
df4e001a07
Renamed to more accurately describe its function.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2248 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-03 17:34:49 +00:00
c2017cc91b
PrintCoverageWalker functionality moved to DepthOfCoverageWalker. Added integration tests.
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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
01cf5cc741
1. Merged CoverageHistogram into DepthOfCoverageWalker
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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
44b9f60735
PercentOfBasesCovered functionality moved to DepthOfCoverageWalker. Added integration tests.
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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
126d1eca35
Move to core (qc/)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2243 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-03 15:45:58 +00:00
9da5cc25ad
More archiving (with permission from Andrey) plus a move to core.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2242 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-03 15:40:27 +00:00
b3bdcd0e60
make sure we close the error log stream in CommandLineProgram if it's opened; unit tests and clean-up for BasicVariation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2241 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-03 06:59:27 +00:00
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.
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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
d7e4cd4c82
Moving some useful and stable walkers to core:
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- ClipReads
- PrintRODs (generalized to print all RODs that are Variations)
- FixBAMSortOrderTag (added documentation to walker so that people know what it does and why)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2238 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-03 03:00:45 +00:00
46f3d3e39b
Added comments to AnalyzeCovariates and R scripts. R script prevents residuals from going off the edge of the plot. Added skeleton code to the recalibration walkers showing how we plan to handle SOLID reference inserting behavior.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2233 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 23:15:52 +00:00
c776f9fb90
Simple utilities for dealing with Complete Genomics data
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2230 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 22:51:41 +00:00
a09fee2b5e
Moved some more walkers to oneoffprojects and killed an old indel-related walker that isn't being used.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2228 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 20:28:07 +00:00
dec0a781c2
Un-reinventing the wheel. --sleep argument removed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2227 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 20:19:28 +00:00
a3343c75db
Move and rename a hybrid-selection-specific coverage calculation to hybridselection/
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2225 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 20:11:22 +00:00
2c83f2f2bc
Move MSG - plus now obsolete classes which it depends on -- to oneoffprojects (with permission from Jared).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2224 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 20:04:22 +00:00
6a9e7bea05
Removing experimental annotations
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2220 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 19:03:55 +00:00
c180a76b05
Added option "append": if set, and the specified discovery output already exists, don't re-call anything that's already present in that file. Append new calls to it.
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Great for resuming long jobs that died partway through.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2219 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 18:56:19 +00:00
0a2304eff8
- Rename minConfidenceScore in VariantEval to minPhredConfidenceScore
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- 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
a5dfc9107d
- Cleaned up annotation code some more
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- Use QualityUtils when phred-scaling now
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2217 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 17:45:29 +00:00
7055a3ea2d
- All annotations are now required to return their VCF INFO keys and descriptions
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- 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
67179e2412
Initial checkin of AnalyzeCovariates.java which replaces analyzeRecalQuals_1KG.py and is updated to use the new Covariates system. It creates similar plots of residual error for each covariate that was used in the calculation. There is also an option to filter out base qualities below a given threshold.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2215 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 16:47:35 +00:00
2838629724
-VCF writer now checks whether the allele frequency has been set before trying to write it out.
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-Renamed methods to be more consistent.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2214 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 16:25:32 +00:00
6231637615
fixes for VariantAnnotations and second bases. Misc. removal of failing (and unstable) integration tests that require rereview
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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
d487428468
remove incorrect parentheses
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2211 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 06:46:32 +00:00
b979bd2ced
- Optimized implementation of -byReadGroup in DoCWalker
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- Added implementation of -bySample in DoCWalker
- Removed CoverageBySample and added a watered down version to the examples directory
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2209 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 03:39:24 +00:00
7c73496e72
Moved DoC walker over to new pileup system so it no longer moves like it's stuck in molasses.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2208 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 02:46:39 +00:00
ba8a8febc6
Thanks to Steve Hershman for finding this bug:
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getNegLog10PError() does not equal the confidence score (you need to multiply by 10 as confidence is traditionally phred scaled). Probably we should change the method to be getNeg10Log10PError(). Anyone have strong feelings on this?
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2207 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 01:59:03 +00:00
3303808a8f
Yet more walkers moved to oneoffprojects.
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Made hybridselection subdir in playground.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2205 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-01 21:29:12 +00:00
05923f7fba
Started transition to oneoffprojects.
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Moved/killed a few other walkers (with permission).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2204 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-01 21:19:02 +00:00
c36069355e
Trivial change to verbose
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2203 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-01 20:48:10 +00:00
74f6526e09
VCFHomogenizer: A class that extends InputStream and dynamically re-writes pilot1 VCF's to be on-spec.
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VCFTool: A command-line tool with various useful VCF functions (validate, grep, concordance).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2202 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-01 17:55:42 +00:00
adf8f1f8b3
Add an InputStream constructor, which is immensely useful for various reasons.
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Also a minor performance optimization.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2201 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-01 17:25:00 +00:00
e581cceab6
Got Kris's permission to delete these walkers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2200 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-01 16:57:28 +00:00
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.
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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
21a9a717e4
Some minor changes and test:
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- 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
084337087e
Removing deprecated code and walkers for which I had the green light from repository.
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Moved piecemealannotator and secondarybases to archive.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2195 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-01 05:58:20 +00:00
2c16c18a04
Move Andrey's old indel code (plus MSG accuracy test, which depends on it) to archive.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2194 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-01 05:29:00 +00:00
7c6c490652
An unfinished implementation of the Wilcoxon rank sum test and a variant annotation that uses it. I need to merge and update this code with Tim's implementation somehow - but that won't happen until later this week, so I'm committing this before I accidentally blow it away.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2193 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-01 04:56:17 +00:00
00f15ea909
Improved performance of deletion-free pileup and added mapping-quality-zero-free pileup convenience method.
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Finished converting genotyper and annotator code to new ReadBackedPileup system.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2192 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-01 04:50:47 +00:00
6bb864da2a
More misc cleanup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2191 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-30 22:29:07 +00:00
b89b9adb2c
misc code cleanup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2190 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-30 21:16:00 +00:00
e793e62fc9
minor code cleanup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2189 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-30 20:57:20 +00:00
4969cb1957
CountCovariates uses new optimized ReadBackedPileup. It also smarter about re-doing calculations for the dnsnp variation rate sanity check.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2188 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-30 20:35:40 +00:00
add2fa7ab4
more use of new ReadBackedPileup optimizations
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2187 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-30 20:04:01 +00:00
817e2cb8c5
Recalibrator makes use of the new GATKSAMRecord wrapper and now no longer has to hash the SAMRecord. Covariate's getValue method signature has changed to take the SAMRecord instead of the ReadHashDatum. ReadHashDatum removed completely.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2185 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-30 19:59:17 +00:00
e9a8156cfb
Use new optimized ReadBackedPileup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2184 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-30 18:17:18 +00:00
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.
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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
a184d28ce9
Completing the optimization started by Matt: we now wrap SAMRecords and SAMReadGroupRecords with our own versions which cache oft-used variables (e.g. platform, readString, strand flag). All walkers automagically get this speedup since the wrapping occurs in the engine.
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I note that all integration/unit tests pass except for BaseTransitionTableCalculatorJava, which is already broken.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2182 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-30 17:39:29 +00:00
af22ca1b47
Bug fixes for VariantEval. dbCoverage now reports dbSNP rate, not some wierd eval_snps_in_db as before. We now separate non-indel and non-snp db sites in dbcoverage. Some dbSNP records don't fit into these two categories. Also fixed a consistency issue where novel / known sites where being determined solely by whether dbSNP had a record there, rather than the stricter dbcoverage screen for isSNP().
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2180 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-30 01:39:01 +00:00
27651d8dc2
Oops. numReads is now called size
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2175 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-29 06:59:17 +00:00
21744e024b
Quick walker that determines % of bases covered at (user - defined depth)x . I've been maintaining it in my directories alone, but now that i've accidentally deleted it twice, into playground it goes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2174 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-29 06:51:19 +00:00
3300ca906a
An iterator for Eric to use when injecting his new wrapping reads -- a stopgap solution for getting additional caching
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functionality into a SAMRecord.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2173 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-27 22:25:52 +00:00
26db15be5c
Added SingleReadGroupFilter to only use reads from a specific read group, filtering out all others.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2172 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-27 20:33:59 +00:00
91f5672a32
misc cleanup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2171 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-27 19:56:20 +00:00
d1298dda13
Encapsulated the sections of code that were shared by the two Recalibration walkers. This includes both the shared command line arguments and the section of code in the map methods which pull out data from the SAMRecord and stuff it into the ReadHashDatum. Command line arguments are now passed to the Covariates using a new initialize method that all Covariates must implement. Updated the dbsnp sanity check warning message to be less cryptic.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2170 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-27 19:54:10 +00:00
75b61a3663
Updated, optimized REadBackedPileup. Updated test that was breaking the build -- it created a pileup from reads without bases...
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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
ac1b289d55
Add tile to ReadHashDatum, and implement TileCovariate
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2166 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-25 21:41:42 +00:00
db40e28e54
ReadBackedPileup in all its glory. Documented, aligned with the output of LocusIteratorByState, and caching common outputs for performance
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2165 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-25 20:54:44 +00:00
b44363d20a
Removed silly casts from Integer to int.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2164 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-25 19:59:21 +00:00
d0f673f0c0
Use Math.abs so we don't get (inconsistent) -0's
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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
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.
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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
cfbd9332b0
small cleanups for the GATK paper genotyper; switched to the managed output system.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2156 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-25 08:04:13 +00:00
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.
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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
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.
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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
2cb3e53b0b
Verbose mode shouldn't be printing out 'NaN's and 'Infinity's
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2153 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 22:01:00 +00:00
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.
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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
3484f652e7
1. Variation is now passed to VariantAnnotator along with the List of Genotypes so non-genotype calls has access to all relevant info.
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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
e05cb346f3
GenotypeLocusData now extends Variation.
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Also, Variations should be INSERTIONs or DELETIONs (and not just INDELs).
Technically, VCF records can be indels now.
More changes coming
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2150 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 21:07:55 +00:00
8b30279edc
style update
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2149 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 20:56:31 +00:00
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.
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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
8fbc0c8473
fix for bug GSA-234: fasta index files couldn't handle anything but letters, numbers, or spaces in the contig name
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2147 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 19:19:47 +00:00
3fca23cd16
Added a stub treeReduce function for debugging multi-threaded execution.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2146 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 18:51:19 +00:00
277e6d6b32
Further optimizations of TableRecalibration. This completes my goal of having the only math done in the map function be addition, subtraction and rounding the quality score to an integer. Everything else has been moved to the initialize method and only done once.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2145 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 18:21:57 +00:00
e4546f802c
Accumulates coverage across hybrid selection bait intervals to assess effect of bait adjacency. Requires input bait intervals that have an overhang beyond the actual bait interval to capture coverage data at these points. Outputs R parseable file that has all data in lists and then does some basic plotting.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2144 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 18:12:34 +00:00
e5106c9924
Hybrid selection performance statistics now include counts of the number of adjacent baits (0,1,2) using OverlapDetector and optionally include assayed bait quantities input via interval lists.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2143 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 18:07:23 +00:00
87c1860398
I'm not sure I believe it, but JProfiler claims that calling FourBaseProbs.isVerbose() was taking 5% of my runtime...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2142 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 17:00:32 +00:00
b3f561710f
Optimizations:
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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
a59e5b5e1a
Added dbSNP sanity check to CountCovariates. If the mismatch rate is too low at dbSNP sites it warns the user that the dbSNP file is suspicious. Added option in CountCovariates and TableRecalibration to ignore read group id's and collapse them together. Also, If the read group is null the walkers no long crash with NullPointerException but instead warn the user the read group and platform are defaulting to some values. Default window size in MinimumNQSCovariate is 5 (two bases in either direction) based on rereading of Chris's analysis.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2140 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 16:16:44 +00:00
e5e6d515c3
Fix misunderstanding of GenomeLoc interval
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2138 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 15:12:49 +00:00
cb6d6f2686
Very minor performance improvements
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2137 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 05:21:07 +00:00
c90bea39a1
read.getReadString().charAt(offset) --> read.getReadBases()[offset]
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[As a courtesy I fixed all instances once I was updating GenotypeLikelihoods]
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2136 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 04:25:19 +00:00
ec321abd7b
Added ability to filter on the QUAL field
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2135 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 04:08:22 +00:00
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.
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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
ee5093d2c6
-Added VariantFiltration integration tests
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-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
be6a549e7b
Added the capability to allow expressions in an integration test command (i.e. -filter 'foo') by escaping them in the command.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2132 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 02:34:48 +00:00
4837fe919c
Convenience changes. If no -BWT option is specified, pull the BWT location from the reference.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2130 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-23 22:46:05 +00:00
9e4eadc37c
CountCovariates v2.0.2: Added a --process_nth_locus <int> argument to only use every Nth covered locus when creating the recalibration table.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2129 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-23 22:07:38 +00:00
ed4cf3de57
Check that we're biallelic before calling isSNP()
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2127 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-23 20:20:48 +00:00
5744a1d968
The covariates don't care about SAMRecord's anymore - Cleaning up the import statements.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2126 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-23 20:10:12 +00:00
23983b2fd8
New annotation: ResidualQuality
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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
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.
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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
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
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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
14bf6ce83c
1. Newest version of the joint estimation model. Faster than previous version and now qscores can get to be > 39.8 for hets.
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2. More sanity checks in annotations
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2119 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-23 17:05:50 +00:00
ee2abd30c4
Count the best alignments and emit them to a file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2118 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-23 16:37:59 +00:00
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
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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
dfe7d69471
1. VCF: don't print slod if it's never set
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2. UG: don't print slod if lods are infinite (todo: figure out a good guess instead)
3. UG: if probF=0 for 2 alt alleles are both 0 (because of precision), use log values to discriminate
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2116 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-23 02:55:43 +00:00
753cb100a3
Add checks for weird situations
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2115 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-23 02:14:25 +00:00
04d6ac940c
Always print out VCF header - not just when there is genotype data present.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2114 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-23 01:44:10 +00:00
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.
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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
b24240664f
Reduced the number of calls to new ArrayList() in TableRecalibration. This results in a speed up of perhaps up to 6 percent (timed trials are hard).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2112 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-22 17:24:31 +00:00
c9c4999354
BWA: odds and ends. Get rid of some spurious debug code that was accidentally
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checked in. Add a better way to write out unmapped reads (thanks Kiran!) Add
a pre-built version of the shared library to the repository for early adoption.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2111 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-22 15:26:07 +00:00
9c206abb97
removing unnecessary printing
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2110 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-22 12:41:48 +00:00
59416ae06a
This is an annotation adapted from one that Mark Daly suggested some time ago. Right now it calculates:
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- For all reference bases, the proportion of their second best bases that support the SNP
- the proportion of non-reference bases that support the SNP
and reports the difference between the two. Initially I was taking depth into account as well, but that did not appear to work as nicely as I'd like (even at 20,000x depth, if 95% of the non-reference bases are C, and 98% of the reference second-best-bases are C, then we would want to be suspicious of it; but perhaps slightly less so than if the depth were only 20...)
Anyway it's now available. I'm not sure how useful it will be, but I spawned the FHS annotation jobs again, so we'll see.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2109 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-22 00:47:49 +00:00
98f921fe24
The refactored CountCovariates now hashes the read object into a HashMap which holds all the properties the covariates pull out of the read over and over again such as read group string, bases string and its complement string, quality scores, etc. This results in a big speed up. CountCovariatesRefactored is now just slightly slower than CountCovariates (perhaps 1.07x according to my latest time trial). Thanks to Alec for suggesting IdentityHashMap. CycleCovariate now warns the user that is is defaulting to the Solexa definition of cycle when the platform string pulled out of the read is unrecognized instead of halting with an Exception.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2108 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-21 20:38:17 +00:00
27122f7f97
Performance improvements for pooled caller. Now possible to actually run on real data in a finite amount of time. Minor changes to GL interface (making strandIndex public) to support cached calculations in pooled caller.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2107 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-21 15:07:40 +00:00
797bb83209
New VariantFiltration.
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Wiki docs are updated.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2105 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-20 19:50:26 +00:00
a78bc60c0f
Minor tweak to improve ease-of-use of iterator system.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2104 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-20 18:24:19 +00:00
4fbb6d05d0
Refactoring. Push the revisions to the common aligner interface down into
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the aligner base classes. Hack the managed implementation to support the
new interface.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2103 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-20 17:08:09 +00:00
d84444200b
The Unified Genotyper now sorts the sample names in the vcf that it outputs.
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[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
38a030f2ba
Finishing off data transfer conduits for single alignment generator.
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Misc bug fixes elsewhere.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2101 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-20 15:21:59 +00:00
2a5349d886
VariantAnnotator now adds dbsnp id if a dbsnp rod is supplied and it's not already set for a record
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2100 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-20 03:26:09 +00:00
b434c1c240
Check for null entries before adding
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2099 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-20 03:12:20 +00:00
82fd824c4d
Continuing improvements to unified genotyper
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2098 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-20 01:39:29 +00:00
33dcfc858d
updates to the paper genotyper based on Mark's comments. There's still more work to do, including more testing.
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Also a 250% improvement in the getBases() and getQuals() of BasicPileup, which was nearly all of the runtime for the genotyper (using primitives instead of objects when possible).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2097 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-19 23:06:49 +00:00
22aaf8c5e0
Added the old recalibrator integration tests to the refactored recalibrator sitting in playground.
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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
a95302fe98
Single alignment generator, another checkpoint. Does generate single alignments, but some of the data still
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needs to plumbed through and it may leak memory.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2095 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-19 21:20:03 +00:00
a972b2769f
Checkpoint. Add first phase of single alignment interface.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2094 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-19 19:03:43 +00:00
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.
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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
b4babb82eb
adding an extra bit of data to come out of CTT (number of chips with actual data)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2091 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-19 17:46:10 +00:00
7623b39927
Add rodPicardDbSNP
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2088 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-19 17:27:46 +00:00
b2b4ff7eca
Cache SAMReadGroup rather than get it twice
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2087 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-19 17:27:18 +00:00
eeb3a3fffb
comments for Aaron
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2081 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-19 12:56:04 +00:00
7997455f38
first go of the genotyper for the GATK paper. More testing and review tomorrow to call it done.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2080 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-19 07:55:24 +00:00
7b957d3e2e
Make the whining from Khalid's office stop already
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2079 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-19 03:04:48 +00:00
85bc9d3e91
(Hopefully) temporary hack: load contig information by contig name rather than contig id to avoid
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off-by-one errors.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2078 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-18 23:33:27 +00:00
0fbd81766b
CountCovariates now uses any rod of type VariationRod with the name dbsnp as the source of known variant sites to skip over. It also grabs the platform string out of the read group when deciding which algorithm to use to calculate machine cycle. In this way it can now handle multi-platform bams. I added a new covariate: PositionCovariate. This is simply the offset regardless of which platform the read came from. This will be useful for comparing between the two covariates. Finally, this message serves as a warning that I will be killing the old recalibrator tomorrow after I've updated and verified new integration tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2077 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-18 23:03:47 +00:00
f667bed7fc
-Don't annotate allele balance or on-off genotype if there's no genotype data
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-If qscore is infinity (because of precision) make a best guess instead
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2076 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-18 22:01:32 +00:00
087e01a439
minor changes for --noSLOD
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2074 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-18 18:48:01 +00:00
a70cf2b763
A bunch of changes needed to make outputting pooled calls possible
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2073 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-18 18:42:57 +00:00
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.
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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
405c6bf2c1
VariantEval genotype concordance for pools! Integration test coming soon
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2071 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-18 17:24:54 +00:00
6fe1c337ff
Pileup cleanup; pooled caller v1
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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
f0a234ab29
TableRecalibration is now much smarter about hashing calculations, taking advantage of the sequential recalibration formulation. Instead of hashing RecalDatums it hashes the empirical quality score itself. This cuts the runtime by 20 percent. TableRecalibration also now skips over reads with zero mapping quality (outputs them to the new bam but doesn't touch their base quality scores).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2069 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-18 16:47:44 +00:00
be31d7f4cc
Added - a walker that outputs relevant information about false negatives given a bunch of hapmap individuals and corresponding integration tests for it.
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This will output for hapmap variant sites:
chromosome position ref allele variant allele number of variant alleles of the individuals depth of coverage power to detect singletons at lod 3 number of variant bases seen whether or not variant was called
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2068 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-18 15:47:52 +00:00
b68d6e06b7
Rollback of the previous "fix" and implementation of the real fix.
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We totally *do* want to annotate the call if called by another walker. Totally boneheaded misenterpretation of what the code was doing -- Eric, please forgive me for being an idiot.
Instead, change the StingException to what it really should be -- an IllegalStateException, which is not coincidentally already handled by the calling function.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2067 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-18 06:09:24 +00:00
95f1be94c0
Fix for the broken build:
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do **not** attempt to annotate if UnifiedGenotyper is called from another walker! Why this didn't break the build earlier I have no idea.
Ultimately, there should be a better way of interfacing UG with another walker -- what if some other walker wants the annotations from UG? But since we're calling map directly -- and the annotations don't get returned directly from map -- this needs to be handled differently, while the map function should ultimately return the LOD score or quality under the GCM alone.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2066 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-18 05:56:31 +00:00
9fb50e9bd9
Further refactoring so that pooled calling will work.
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Okay, Mark, you should be all set.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2065 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-18 00:18:13 +00:00
539f6f15e5
Added --
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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
42a0bbaf46
Minor reformating for pooled calling
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2063 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-17 22:06:11 +00:00
ec1a870905
Working with byte arrays is faster than working with Strings so the Covariates now take in byte arrays. None of the Covariates themselves used the reference base so I removed it. DinucCovariate now returns a Dinuc object which implements Comparable instead of returning a String because it was too slow. CountCovariates now uses a read filter to filter out unmapped reads and allows the user to specify -cov all which will use all of the available covariates, of which there are 7 now. If no covariates are specified it defaults to ReadGroup and QualityScore, the two required covariates. Initial code in place to leave SOLID bases alone if they have bad color space quality. TableRecalibration uses @Requires to tell the GATK to not give the reference bases since they weren't being used for anything.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2062 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-17 21:50:52 +00:00
4d9c826766
Integration tests actually run on real data now.
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<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
a048f5cdf1
-Refactored JointEstimation code so that pooled calling will work
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-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
43bd4c8e8f
Ignoring deletions in the primary pileup by default was causing the primary pileup to become shorter than the secondary pileup when building up the secondary base pileup string. This fix makes sure to include the primary Ds within the pileup so that not only are the pileups guaranteed to be the same size, the same offsets will truly correspond with the same read.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2058 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-17 17:20:13 +00:00
aece7fa4c7
a convenience method to join a map into a single string, which I need for some VCF work. Added some documentation to the join method as well.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2057 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-17 16:50:01 +00:00
21729d9311
Do not print debug message when debug mode is not requested!!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2056 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-16 20:28:41 +00:00
967215066d
The old CountCovariates now warns the user if they didn't supply a dbSNP rod file. Thanks Kiran for the use case.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2055 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-16 19:16:46 +00:00
eb07c7f7f8
CountCovariates now warns the user if they didn't supply a dbSNP rod file. Thanks Kiran for the use case.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2054 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-16 18:44:54 +00:00
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.
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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
ce5034dc5d
Finally reinstate the iterator-style interface. Get rid of some scaffolding code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2052 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-16 02:34:19 +00:00
103763fc84
An accessor for the VCF header
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2051 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-15 09:28:25 +00:00
97ed945797
Example code for a bug in the VCF implementation. See JIRA entry at http://jira.broadinstitute.org:8008/browse/GSA-225
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2050 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-15 09:27:12 +00:00
88fd762436
The -rf argument is now being used for read filter and is colliding with my walkers. Changed mine to -recalFile
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2048 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-14 19:37:46 +00:00
b05119987c
Clarified some of the comments in the individual covariates now that things have been moved around to speed up the code. In general most error checking and adjustments to the data are done per read instead of per base. This means that functionality was moved out of the covariate modules and into CovariateCounterWalker and TableRecalibrationWalker.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2047 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-14 18:44:05 +00:00
672472789e
Added some documentation to the helper classes. Fixed an error case in TableRecalibrationWalker.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2046 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-14 18:13:43 +00:00
15c14add4d
Repackage the aligner for better partitioning. The C aligner, for example, is now
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partitioned from the Java aligner, and both are partitioned from the more general-
purpose BWT reader.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2045 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-13 22:55:27 +00:00
d1b525b428
Default window size for NQS covariate is 3
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2040 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-13 19:24:27 +00:00
394c839974
Implemented NQS covariate. Extended Cycle covariate to handle 454 and SOLID reads. Added a Primer Round covariate for SOLID reads.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2039 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-13 19:22:21 +00:00
bf451873ff
1. Bug fix: check that AF=0 doesn't contain more probability than 1-fraction
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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
1be36ca959
Bug fix: when cleanedReadIterator is initialized, it gets immediately set to the contig of the first cleaned read; when the first uncleaned read coming in is on the lower contig, this would trigger 'readNextContig' with that lower contig as an argument. As the result, the whole cleaned reads file would be read through the end and no cleaned reads would be ever seen by the code afterwards. Now we do not call readNextContig if the (uncleaned) read's contig is lower than the current contig already loaded into cleanedReadIterator. the 'readNextContig' method now also throws an exception if requested contig is less than the currently loaded one
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2037 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-13 15:41:26 +00:00
b1376e4216
structure refactored throughout for performance improvements
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2036 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-13 15:41:09 +00:00
cff31f2d06
comments for eric
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2035 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-13 14:19:31 +00:00
234bb71747
changed the toVariation() method to take a reference base, instead of using the reference base loaded from the underlying data source (if it was reference aware). Also changed some isVariant() methods which weren't using the passed in ref base.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2034 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-13 06:54:38 +00:00
902cf84448
Bug fix: if the most likely allele frequency is 0, don't make a variant call (even if the Qscore for AF=1/n > threshold)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2033 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-13 04:10:32 +00:00
555fb975de
1. Print out allele frequency range (from joint estimation model only).
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2. Don't print verbose output from SLOD calculation (it's just a repeat of previous output).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2032 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-13 03:59:13 +00:00
72825c4848
A walker that generates a table of secondary base counts in a bam file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2031 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-13 02:11:23 +00:00
8145ed4672
Take 2, updating picard with bug fix for bam files containing no reads.
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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
61b5fb82ce
2 major changes:
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1. Add dbsnp RS ID to VCF output from genotyper; to do this I needed to fix the dbsnp rod which did not correctly return this value.
2. Remove AlleleBalanceBacked and instead generalize the arbitrary info fields backing VCFs (and potentially others) in preparation for refactoring VariantFiltration next week.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2028 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-12 22:51:49 +00:00
3742a05760
Now can read E2 or SQ tag.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2027 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-12 15:18:21 +00:00
c3c001e02e
cleanup of the traversal output code
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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
0922400ca9
Don't try to calculate ratios when DoC is zero (which happens when calls are made by an LD-aware genotyper)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2025 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-12 02:51:44 +00:00
697d7e02c8
Remove the lazy initialize functionality. When no calls are made by the genotyper, we still want a vcf file to be output with valid header.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2024 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-12 02:14:50 +00:00
2ea85fb62b
Fix some problematic command-line argument naming and descriptions.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2023 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-12 02:12:26 +00:00
0c2a957ae0
Better configuration support. Now supports everything that people have expressed interest in except edit distance.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2021 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-11 20:54:49 +00:00
6c9f86bb4d
Removed unnecessary output and added debugging print() routine
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2020 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-11 18:37:36 +00:00
578dcc54a4
Don't create a record if ref=N
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2018 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-11 04:32:17 +00:00
8406325247
New Picard is breaking one of the integration tests.
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Revert until we find out whether the cause is legit.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2017 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-11 03:59:32 +00:00
499e7d1d75
Push forward some more delicate merging routines.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2016 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-11 03:07:34 +00:00
bae4d3f7ea
Updated Picard with fix for Doug Voet. Thanks Alec.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2015 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-11 02:01:08 +00:00
2e4782f202
Command-line arguments for SamReadFilters.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2014 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-10 23:36:17 +00:00
a13cbe1df0
The refactored recalibrator now passes the integration tests as well as my own validation tests. I'm ready to have other people start jamming on the files. I'll make an updated wiki page soon. The refactored recalibrator is currently a bit slower than the old one but there were a lot of great, easy ideas today for how to improve it.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2013 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-10 22:20:06 +00:00
2cf9670d1e
Allow users to directly specify filters from the command-line, applicable to
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any walker.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2012 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-10 18:40:16 +00:00
6a37090529
Output changes for VCF and UG:
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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
1e7ddd2d9f
Added a validateOldRecalibrator option to CovariateCounterWalker which reorders the output to match the old recalibrator exactly. This facilitates direct comparison of output. Changed the -cov argument slightly to require the user to specify both ReadGroupCovariate and QualityScoreCovariate to make it more clear to the user which covariates are being used. Some speed up improvements throughout.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2010 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-10 15:55:56 +00:00
7e30fe230a
oops, missing file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2009 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-10 13:25:18 +00:00
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
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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
f9819d5f13
a little clean-up
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2007 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-10 06:18:34 +00:00
2ed423ed56
print the current location in read walkers (in addition to the number of reads processed), along with some refactoring to support the change.
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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
c9c3cf477a
Based on feedback from Kiran, we know uniquify sample names as sample.rodName (instead of sample.1, sample.2, ...)
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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
2fa2ae43ec
Enough people have found this useful, so...
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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
3793519bd4
-Added convenience method to VCF record to tell if it's a no call and have rodVCF use it before querying for info fields
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-Don't restrict info fields to 2-letter keys
[about to move these to core]
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2002 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-09 20:52:51 +00:00
740a5484c4
Added some documentation to the code, mostly especially to CovariateCounterWalker but various comments added throughout. Also changed the HashMap data structure to accept an estimated initial capacity. This had a very modest improvement to the speed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2001 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-09 20:13:56 +00:00
74751a8ed3
-Some minor fixes to get accurate vcf record merging done
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-Improvement to snp genotype concordance test
And with that, it looks like I get revision #2000 .
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2000 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-09 06:40:55 +00:00
ab705565cf
Completely refactored the Callset Concordance code. Now, it takes in VCF rods and emits a single VCF file which has merged calls from all inputs and is annotated (in the INFO fields) with the appropriate concordance test(s).
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Still needs a bit of polish...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1999 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-09 05:03:13 +00:00
bc6f24e88f
Added VCFUtils which contains some useful VCF-related functions (e.g. ability to merge VCF records).
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Also, various minor improvements.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1998 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-09 04:53:32 +00:00
cff645e98b
convenience method to deal with genotypes that are unsorted (e.g. CA vs. AC)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1997 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-09 04:45:49 +00:00
7fde6c0bf4
One more output tweak.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1996 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-09 04:42:55 +00:00
00a7113d7a
Tweaks to formatting of output table.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1995 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-09 04:33:36 +00:00
7ce0df76f8
Added accessors to the rod data sources so that walkers can access the name/file/type triplets for input rods. This is necessary if e.g. you want to create a vcf writer based on all of the samples being input.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1994 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-09 04:25:39 +00:00
d07f3bb6f6
Added methods to get strand bias and to test if record has allele freq or bias fields set.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1993 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-09 04:20:35 +00:00
3313b0ddb4
Fixed a minor bug where the lodThreshold wasn't being printed in the header.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1992 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-08 16:51:36 +00:00
95d381efe2
Optionally computes the error rate using the best base and a random base.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1991 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-08 16:47:34 +00:00
567f5758d2
Optionally lists read depths by read group.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1990 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-08 16:39:19 +00:00
a679bdde18
FindContaminatingReadGroupsWalker lists read groups in a single-sample BAM file that appear to be contaminants by searching for evidence of systematic underperformance at likely homozygous-variant sites.
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Procedure:
1. Sites that are likely homozygous-variant but are called as heterozygous are identified.
2. For each site and read group, we compute the proportion of bases in the pileup supporting an alternate allele.
3. A one-sample, left-tailed t-test is performed with the null hypothesis being that the alternate allele distribution has a mean of 0.95 and the alternate hypothesis being that the true mean is statistically significantly less than expected (pValue < 1e-9).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1989 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-08 16:36:39 +00:00
2225d8176e
A convenience class for maintaining a dynamically growing table of values with access to the elements by named row and column identifiers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1988 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-08 16:34:35 +00:00
21c5f543fa
Fix sharding bug -- loci to which >100,000 (= 1 shard) reads are assigned an
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alignment start will confuse the sharding system and cause it to return duplicate reads.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1987 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-08 14:27:26 +00:00
84ba604611
Sequential quality score calculation is now in place in the refactored recalibrator and matches the quality scores calculated by the old recalibrator exactly; at least on the small sets of data used so far. Validation, documentation, and optimization work is on going.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1985 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-07 15:55:16 +00:00
bf1bc94060
Fixes for PooledConcordance bugs and lack of safety checking
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1984 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-07 01:54:10 +00:00
66d4a995e6
Initial check in of refactored Recalibrator. The new walkers are called CountCovariatesRefactored and TableRecalibrationRefactored. More work is needed to finish up the sequential calculation and to document the code sufficiently. These files are not ready to be used by other people quite yet.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1982 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-06 22:33:55 +00:00
6fdfc97db6
Added optional field DP to VCF output for Mark.
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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
0a55fa5bb1
Completely refactored the Genotype Concordance module(s).
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Now PooledConcordance and GenotypeConcordance inherit from the same super class (and can therefore share data structures and functionality). Also, they now use ConcordanceTruthTable to keep track of necessary info.
GenotypeConcordance passes integration tests.
PooledConcordance needs to be finished by Chris.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1979 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-06 16:27:16 +00:00
d549347f25
Refactored GenotypeLikelihoods to use an underlying 4-base model.
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It needs to be modified a bit and then hooked up to a pooled model, but that is now possible.
At this point, there is no difference to the Unified Genotyper.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1978 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-05 21:59:25 +00:00
4d3871c655
don't flush anymore.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1977 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-05 19:11:51 +00:00
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.
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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
43c3ee61d5
Fix minor mapping quality bug.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1973 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-04 14:33:23 +00:00
a545859c62
Joint Estimation model now emits a reasonable slod
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1969 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-03 21:12:42 +00:00
11d950abe0
No longer allow the lod_threshold argument - use confidence instead.
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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
2fb45dbd73
Make window size a command line argument
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1967 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-03 16:13:35 +00:00
55f61b1f88
Bug fix in adjustment of the shift position.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1966 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-03 16:08:11 +00:00
5d5dc989e7
improvements to VCF and variant eval support of VCF -- now listens to the filter field
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1963 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-03 12:09:30 +00:00
c63af32fc7
The BWA/C bindings were triggering the local aligner to repeatedly reload the
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ref genome. Make sure the reference genome is cached.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1961 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-03 00:01:55 +00:00
3a33401822
2nd stage of the genotyper output refactoring is complete.
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Now, all output is generalized and all of the intelligence lies where it is supposed to.
Next stage is syncing up old and new models and making sure we're outputting exactly what we should.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1960 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-02 22:43:08 +00:00
ba67c7f02b
added a warning for those using bed files; we properly convert bed to the internal representation but the user needs to be aware that any output will be one-based closed intervals
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1959 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-02 21:09:18 +00:00
b71b66bd88
the underlying parameter is a float so we need to use Float.valueOf() instead; Noticed by external user Hou Huabin
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1958 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-02 20:22:25 +00:00
5a510e6d98
New PackageUtils interferes with the packaging utility. Revert until Aaron and
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I can get together to make this work.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1957 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-02 19:14:14 +00:00
de6ae51f7e
Scala walkers can now be build and run like any other walker in the GATK. Added the getUrlsForClasspath to PackageUtils, the Reflections package isn't getting the manifest files from jars in the classpath, and so we weren't seeing any walkers outside of the GenomeAnalysisTK.jar.
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A couple of notes:
-Commented out BaseTransitionTableCalculator.scala because it's won't build; Chris could you fix this one (or kill it if it's not needed).
-Removed the PrintReadsScala walker; moved the code over to a ScalaCountLoci walker (which is what the code was really doing).
-Added configurations items to the ivy xml file.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1956 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-02 06:02:41 +00:00
1896f334d9
Fixed collection of bugs in reads aligning to multiple locations.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1955 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-02 04:02:09 +00:00
af6d0003f8
-Generalized the GenotypeConcordance module to deal with any number of individuals (although it will default to its old behavior if the -samples argument is left out).
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-Make rods return the appropriate type of Genotype calls from getGenotype().
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1954 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-01 05:35:47 +00:00
b95165e39c
Make alignment (temporarily) part of main GenomeAnalysisTK.jar. Add some extra logging errors on failure.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1953 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-01 00:33:18 +00:00
4b0796ba58
After fixing a few glitches and bugs, this version finally works as intended
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1952 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-31 04:59:58 +00:00
7d0ac7c6f2
Fix for long-term VariantEval bug plus new intergration test to catch it
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1951 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-31 00:00:33 +00:00
ea8d5c7077
Some internal refactoring. Now "safely" ignores duplicate records (NOT duplicate reads but rather malformed bam files!) resulting from the bug/feature in CleanedReadInjector.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1949 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-30 17:50:51 +00:00
a3da475c88
Documentation and cleanup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1946 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-30 15:40:28 +00:00
2d15891719
Created walkers for alignment, validation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1945 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-30 15:04:07 +00:00
51fffc7f69
Comments for Ryan (which also apply to ReadQualityScoreWalker).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1944 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-30 14:44:04 +00:00
ccd7440730
We can actually make this a bit simpler (and faster)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1943 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-30 04:21:03 +00:00
1b6333e4ab
Enough people have asked for this that it just needed to get written.
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One can now split up any number of sets into an N-way Venn (although it doesn't check for discordance in the calls, so you'll still want to use SimpleVenn for 2-way comparisons).
Wiki docs are updated.
To do: update to use Ryan's generic hash map when it's ready for public use.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1942 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-30 04:08:45 +00:00
4bdb5b03bd
tell UnifiedGenotyper to return calls at all bases
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1941 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-30 03:10:44 +00:00
4ee1d6f733
-Have the calculation models determine whether a call passes the lod/confidence thresholds (as opposed to returning everything and letting the UG decide); this way, walkers which call map() will get only the good calls.
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-Do the right thing in all models for all-base-mode (for Kiran).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1940 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-30 02:35:51 +00:00
64ac956885
Okay, I caved in:
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CallsetConcordance now gets possible concordance types by looking at classes that implement ConcordanceType instead of having them hard-coded in.
Thanks to Kiran this was pretty easy...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1939 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-30 00:32:26 +00:00
1f0d852a48
Fix bug where alignments with indels would be busted because bwa reverses
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the read bases to undo a previous read base reverse that doesn't occur in the
libbwa codepath.
Also fixed some memory management issues.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1938 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-29 21:33:13 +00:00
e3b4d4cbed
Genotyper reimplemented. Does the same thing, at least for now, but internal data structures redesign enables collecting various statistics for indel-containing/reference-matching reads. The statistics are not yet used by the caller itself to make a better judgement w.r.t. the validity of the calls it makes, but they are now printed into the output stream (--verbose). The statistics (for both normal and tumor) include: indel observation count/total coverage, av. number of mismatches per indel-containing and per ref-matching read, av. mapping quality, av. mismatch rate and av. base quality within an NQS windoew around the indel, numbers of indel and ref observations per strand.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1936 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-29 19:09:16 +00:00
f04b80d7db
Fixed epic memory leak.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1934 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-29 16:32:43 +00:00
1c4ca9d383
-Mark just reminded me: actually force the ref/loc to be immutable
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-VCF writer should be blind to the score/confidence/lod value - just print the thing out as is
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1932 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-29 13:41:53 +00:00
5cdbdd9e5b
now that the design is stable, pull the setReference and setLocation methods back out of Genotype and stick them into constructors of implementing classes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1931 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-29 13:27:37 +00:00
3091443dc7
Sweeping changes to the genotype output system, as per several discussions with Matt & Aaron.
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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
86573177d1
Reverting rod walkers to use underlying refwalker implementation while we work on ROD2 and reenable the system. Added some serious sparse file parsing to variant eval tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1929 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-29 01:04:37 +00:00
c9a3707cfd
Initial version of BWA/C bindings. Still lots of squirrels roaming the code.
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- Some cigar strings aren't right.
- Memory leaks.
- BWA codebase changes aren't committed to BWA tree.
- Aligner interface butchered to support BWA/C-style alignments.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1928 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-28 21:37:49 +00:00
c4359bc340
Whoops. Forgot the implements.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1927 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-28 19:59:57 +00:00
5a3bd50537
adding error log reporting to the GATK, and a stream based output method for the argument collection
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1926 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-28 19:56:05 +00:00
863d3023d5
IndelCounterWalker -- a new little walker that counts indels over a region (want to see what kind of havoc BWA may be resulting in). Don't know when BasicPileup.indelPileup() was written, but kudos to whoever wrote it.
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BTTJ - remove 'N's from previous base analysis -- even if both read and ref are 'N' (which does happen, occasionally)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1925 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-28 19:50:50 +00:00
04e9a494e9
removed the GenotypesBacked interface, which is currently unused. Also cleaned up some documentation lines
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1924 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-28 18:08:14 +00:00
06ff81efe5
Added NeighborhoodQualityWalker.java and ReadQualityScoreWalker.java which are used to calculate a read quality score based on attributes of the read and the reads in the neighborhood.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1922 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-28 13:24:11 +00:00
68fa6da788
Initial graph-based reference implementation and alignment assessor. Not suitable for public use
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1921 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-27 21:54:47 +00:00
31d143a841
now only needs READS
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1920 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-27 21:54:14 +00:00
ef2ea79994
code cleanup and containsStartPosition function
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1919 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-27 21:53:40 +00:00
186a8dd698
Trivial protection for null value
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1918 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-27 21:52:52 +00:00
be333da9c0
charSeq2byteSeq -- convert a char[] to a byte[] for convenience
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1917 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-27 21:52:23 +00:00
4192b093b8
More robust error handling with parallelization + usePreviousBase. Added forceReadBasesToMatchRef to use in conjunction with nPreviousReadBases as a less stringent approximation of usePreviousBases (requiring previous pileups only had mismatches, and that read mapping quality be high was throwing everything away)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1916 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-27 17:20:44 +00:00
31d5df2859
Previous base now checks that the read matches the reference in the previous base window.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1915 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-27 15:58:20 +00:00
726378be8b
Almost ready to stop doing eagar decoding; waiting on Eric
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1914 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-27 15:28:05 +00:00
e96b1791ab
Need to check for biallelic snp or exception gets thrown.
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Also, update to new tracker calls.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1913 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-27 02:43:43 +00:00
3fb3773098
a fix for traverse dupplicates bug: GSA-202. Also removed some debugging output from FastaAltRef walker
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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
a1e8a532ad
Support for initialize() and onTraversalDone() output from parallelized walkers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1911 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-26 20:18:31 +00:00
62c1001790
BTTJ is now correct. What a terrible waste of time, turns out I'd just reversed the header. Because of this the MD5 had to be updated in the tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1910 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-26 19:24:18 +00:00
24c7f694e6
Handles allele frequencies for any specified population, changed user input for mismatch filter options
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1909 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-25 22:51:56 +00:00
db9419df49
@ Hack to allow output from onTraversalDone()
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1908 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-25 15:19:04 +00:00
75ad6bbef7
Check that map isn't being called passing in null arguments.
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(This seems wrong; see JIRA entry GSA-211)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1907 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-25 02:30:36 +00:00
b4f55df600
Bugfix for Jason F
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1906 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-24 22:09:27 +00:00
65b98470f3
Temporary fix: have RodLocusView manage and close its RODs. Really the
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relationship between these two classes needs to be rethought; see JIRA
GSA-207.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1904 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-23 16:00:12 +00:00
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.
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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
6c338eccb8
Joint Estimation model now emits calls in all formats.
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The whole GenotypeCall framework needs to be changed, but this will work for the time being.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1902 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-23 03:07:28 +00:00
a6dc8cd44e
BTTC is now Tree Reducible allowing for parallelization.
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Integration test comment changed to reflect actual date of last md5 update.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1901 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-22 23:19:29 +00:00
2e552eb5a1
Validates intervals against sequence dictionary header bounds.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1900 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-22 19:31:15 +00:00
54c61c663c
-Cleanup of the Joint Estimation code
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-Don't print verbose/debugging output to logger, but instead specify a file in the argument collection (and then we only need to print conditionally)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1899 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-22 15:25:29 +00:00
2cab4c68d4
Added method: isCodingExon(). Returns true if position is simultaneously within an exon AND within coding interval of any single transcript from the list. The old method of detecting coding positions as isExon() && isCoding() is buggy, as the position could be in the UTR part of one transcript (isExon() is true), and within coding region bounds (but not in the exon) of another transcript (isCoding() is true). As a result UTR positions would be erroneously annotated as coding.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1898 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-22 14:55:07 +00:00
af761fb9bd
Base transition table now forces epsilon/3 (three-state) model for the unified genotyper. Verified to be identical with changing the default model to being epsilon/3. This of course changes the observed counts, so the integration test has been updated.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1897 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-21 21:18:26 +00:00
55fa1cfa06
-Renamed new calculation model and worked out some significant xhanges with Mark
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-Allow walkers calling the UG to pass in their own argument collections
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1896 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-21 20:49:36 +00:00
8e3f72ced9
BTTJ - Code refactoring (major) - passes integration test
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VariantEvalWalker - whoops, wrote PooledGenotypeAnalysis rather than PooledAnalysis, now passes tests again
- PooledFrequencyAnalysis - don't bother initializing matrices if this isn't a pool
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1895 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-21 19:04:51 +00:00
15a1849758
notes for chartl
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1894 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-21 18:31:31 +00:00
77863d4940
@PowerBelowFrequency
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+ Changes to doc
@ BasicPoolVariantAnalysis
+ use char rather than ReferenceContext
+ calculate # alleles
@ PooledFrequencyAnalysis
+ breakdown of call metrics by estimated number of alleles in pool
@ VariantEvalWalker
+ add PooledFrequencyAnalysis to analysis set
@ PooledGenotypeConcordance
+ correctly calculate maximal allele frequency for output
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1893 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-21 15:17:11 +00:00
967128035e
Make command like args default to false.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1892 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-21 13:59:35 +00:00
9b9744109c
Mark's new unified calculation model is now officially implemented.
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Because it doesn't actually use EM, it's no longer a subclass of the EM model.
Note that you can't use it just yet because it doesn't actually emit calls (just prints to logger). I need to deal with general UG output tomorrow. Hold off until then, Mark, and then you can go wild.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1891 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-21 02:39:23 +00:00
caa3187af8
Enabling correct high-performance ROD walker and moved VariantEval over to it. Performance improvements in variantEval in general. See wiki for full description
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1890 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-20 23:31:13 +00:00
4a8a6468be
Use read group as a condition for confusion tables. With an integration test.
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Changed BaseTransitionTable to comparable objects for consistent ordering of output
( e.g. so the integration test doesn't yell so much )
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1889 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-20 19:39:32 +00:00
b83df5616a
Change for lower-case references (always compare upper case bases)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1888 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-20 17:36:31 +00:00
3b1fabeff0
Major code refactoring:
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@ Pooled utils & power
- Removed two of the power walkers leaving only PowerBelowFrequency, added some additional
flags on PowerBelowFrequency to give it some of the behavior that PowerAndCoverage had
- Removed a number of PoolUtils variables and methods that were used in those walkers or simply
not used
- Removed AnalyzePowerWalker (un-necessary)
- Changed the location of Quad/Squad/ReadOffsetQuad into poolseq
@NQS
- Deleted all walkers but the minimum NQS walker, refactored not to use LocalMapType
@ BaseTransitionTable
- Added a slew of new integration tests for different flaggable and integral parameters
- (Scala) just a System.out that was added and commented out (no actual code change)
- (Java) changed a < to <= and a boolean formula
Chris
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1887 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-20 14:58:04 +00:00
4be6bb8e92
added a check to ensure the eval track variation is bi-allelic. Also changed some string constants over to enums. For some reason my check-ins from home wouldn't work last night, so this is the actual changes for 1884.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1886 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-20 14:15:33 +00:00
449a6ba75a
Deleting lots of code as part of my cleanup. More classes tagged for removal. Many more walkers have their days numbered.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1885 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-20 12:23:36 +00:00
d749a5eb5f
added a check to ensure the eval track variation is bi-allelic. Also changed some string constants over to enums
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1884 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-20 04:56:51 +00:00
b8ab77c91c
Don't filter out reads without proper read groups. Instead, allow the user (or another walker calling UG) to specify an assumed sample to use (but then we assume single-sample mode).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1883 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-20 01:30:53 +00:00
a8a2c1a2a1
Replaced SSG with UG in packaging utils. Minor performance and formatting improvements for ClipReads
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1882 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-20 01:19:58 +00:00
c29924e7cf
Reverting previous change.
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Aaron, it's all yours...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1881 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-20 00:55:24 +00:00
d21b582b18
memory leak, where the Resource Pool was releasing based on the value and not the key, resulting in the resourceAssignments map growing with each additional shard
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1880 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-20 00:39:42 +00:00
761a730758
assertBiAllelic -> assertMultiAllelic.
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Chris, if this breaks an integration test, you get it.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1879 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-20 00:09:46 +00:00
2a26bb42dd
Softclipping support in clip reads walker. Minor improvement to WalkerTest -- now can specify file extensions for tmp files. Matt -- I couldn't easily create non-presorted SAM file. The softclipper has an impact on this.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1878 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-19 21:54:53 +00:00
055a99fb05
Change in ordering for a disjunctions. Walker will no longer try to calculate number of simple mismatches in the pileup if the pileup includes 'N's.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1877 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-19 18:24:14 +00:00
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
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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
3d50c72d74
Forgot a dumb little System.out.println. You will be flooded with "This read will not be used." statements until, overwhelmed, you give in to my demands.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1874 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-19 16:13:48 +00:00
225ef52973
Now produces same output as the Scala walker for unconditioned tables (no 2bb, no previous base, etc.)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1873 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-19 16:10:44 +00:00
51f9ec0a5c
subtract largest posterior value from all values; this hopefully solves any precision issues
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1870 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-18 05:20:15 +00:00
b9e8867287
-push allele frequency and genotype likelihood variable definitions down into the subclasses so that they can use different data structures
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-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
d6385e0d88
simpleComplement function() in BaseUtils. Generic framework for clipping reads along with tests. Support for Q score based clipping, sequence-specific clipping (not1), and clipping of ranges of bases (cycles 1-5, 10-15 for example). Can write out clipped bases as Ns, quality scores as 0s, or in the future will support softclipping the bases themselves.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1868 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-16 22:29:35 +00:00
ad777a9c14
@BasicPileup - made the counts public so they can be used
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@PoolUtils - split reads by indel/simple base
@BaseTransitionTable - complete refactoring, nicer now
@UnifiedArgumentCollection - added PoolSize as an argument
@UnifiedGenotyper - checks to ensure pooled sequencing uses the appropriate model
@GenotypeCalculationModel - instantiates with the new PoolSize argument
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1867 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-16 21:56:56 +00:00
bdb34fcf38
Updated integration tests for VariantEval. Hooray for IT!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1866 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-16 20:00:29 +00:00
85a4fbc256
Bumping version of Picard for firehose compatibility.
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Integration tests were validated against svn rev 1861, before the wonder
twins committed their changes.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1864 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-16 19:38:56 +00:00
8aacc43203
VCF output now emits no calls as ./.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1863 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-16 18:51:31 +00:00
d1a4cd2f73
Added ValidationData analysis type to VariantEvalWalker; this eval takes a GFF file with validated truth data positions (bound to "validation")and calculates the accuracy of the genotype calls bound to "eval".
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1862 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-16 15:39:08 +00:00
418e007ca6
A cleaner interface: now everyone can use UG's initialize method
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1860 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-16 14:09:16 +00:00
96972c3a5c
a fix for a bug Eric found: if your first call contains fewer samples than calls at other loci, your VCFHeader got setup incorrectly.
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Also moved a buch of Lists over to Sets for consistancy.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1859 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-16 04:57:50 +00:00
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.
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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
b82c3b6040
Better error output (and fixed spelling mistakes)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1857 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-16 01:01:45 +00:00
993c567bd8
I had to remove some of my more agressive optimizations, as they were causing us to get slightly different results as MSG. Results in only small cost to running time.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1856 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-16 00:59:32 +00:00
7d7ff09f54
throw an exception if read has no associated read group
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1855 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-15 18:11:32 +00:00
b9544d3f89
Output formatting change (very slight)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1854 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-15 16:47:29 +00:00
839c5d66bc
Read uints directly into longs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1853 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-15 16:15:11 +00:00
ce38fa7c81
Breaking the signed int glass ceiling; stage 1: convert critical ints to longs. Code cleanup and documentation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1852 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-15 15:28:56 +00:00
79993be46c
changed blank gene name to UNKNOWN
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1851 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-15 13:47:00 +00:00
0c2016c19a
Improved error messages -- now easier to read, points to the GATK Error Messages wiki, and avoids double printing of stack traces
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1850 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-15 12:07:44 +00:00
a9094c835c
clean-up and fixes to the VCF input
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1849 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-15 04:53:59 +00:00
a32470cea1
Deal with the fact that walkers can call UG's init/map functions directly.
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We need to filter contexts in that case since the calling walkers don't get UG's traversal-level filters.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1848 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-15 02:31:45 +00:00
8dca236958
Base-packed reader cleanup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1847 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-15 01:26:23 +00:00
316b30ee56
On the road to human: make sure the suffix array will fit in a Java array.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1846 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-14 21:45:35 +00:00
depristo
rpoplin
ebanks
andrewk
aaron
chartl
asivache
hanna
alecw
kiran
jmaguire
sjia
mmelgar
kcibul