a40e64e47b
A downsampling validator. Compares the generated pileup passed in from the alignment context to the reads,
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passed in as a Tribble SAM text feature. If the generated pileup contains a valid set of reads according to
the downsampling rules, the test passes.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3421 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-23 21:49:54 +00:00
a280a0ff0d
a) Made HaplotypeScore default annotation. This changed several integration tests, whose MD5 is now updated.
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b) Disabled BaseQualRankSumTest, the returned p-values differ wildly from Matlab/R-provided ones, cause TBD.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3419 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-21 22:25:17 +00:00
b10950c691
Simple performance optimization -- cache the number of reads in the locus hanger.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3417 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-21 19:26:16 +00:00
7fb3f2d3eb
Annotator now buffers indel calls (prevents double-output from double-calls to map)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3413 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-21 16:34:34 +00:00
4e834b5e35
VFW now uses a ref window and thus is compatible with indels.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3412 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-21 15:59:42 +00:00
88cb93cc3c
Changes to Depth of Coverage (added maximum base and mapping quality flags; with new integration tests -- because they use b36, and the other test uses hg18, it's in a different class (integration test system can't change refs on the fly). Initial change to VariantAnnotator to allow it to see extended event pilups; you currently have to throw the -dels flag; and it's specified as "very experimental". Yet,all the integration tests pass.
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Homopolymer Run now does the "right" thing (e.g. single bases are represented as HRun = 0 rather than HRun = 1) for indels. AlleleBalance now does something close enough to correct.
Added a convenience method to VariantContext that will return the indel length (or lengths if a site is not biallelic).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3409 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-21 13:02:01 +00:00
6faf101c6c
Minor improvements to Callable Loci for public consumption
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3408 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-21 12:50:11 +00:00
388dd8d64d
Fixing bugs in downsampler introduced when I added Ryan's dup eliminator.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3407 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-21 02:53:12 +00:00
a10fca0d5c
Genotyper now is using bytes not chars. Passes all tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3406 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-20 21:02:44 +00:00
7389077b3b
A few misc usability fixes:
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- Clarify the message emitted when -XL is supplied so I don't spend another half day chasing a bug that doesn't exist.
- Crash with a helpful message when running -nt with non-TreeReducible walkers.
- Crash with a helpful message when running -nt with reduceByInterval walkers.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3405 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-20 19:02:02 +00:00
b543dd4ac4
more aggressive checks for the locking, and some more documentation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3404 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-20 16:16:36 +00:00
727822adb4
BaseUtils has more clear distinction between byte and char routines. All char routines are @Depreciated now. Please use bytes. Better organization of reverse(), now in Utils not BaseUtils.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3400 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-20 14:05:13 +00:00
6ce3835622
Removing unused methods in QualityUtils; ReferenceContext now converting all bases to upper case, but can be disabled with static boolean
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3399 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-20 12:38:06 +00:00
5abac5c057
A few more char -> byte cleanups
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3398 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-20 00:02:06 +00:00
8a725b6c93
Restructuring of ReferenceContext and ReadWalkers to accept a ReferenceContext. Now ReferenceContext is byte[] backed not char[]. Please no more chars for the reference. All of the tests pass now. Coming check-ins are going to clean up the char / byte problems in the GATK
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3397 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 23:27:55 +00:00
02cc1afdc8
remove RodBed and all it's dependencies.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3396 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 19:12:30 +00:00
0036df7b03
adding a convenience method for getting at the RODs that overlap a specific locaiton as GATKFeatures.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3394 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 17:40:20 +00:00
ca386439be
only emit a warning if the tribble index is out of date, don't remove and replace it for them. Added a test case where the log4j appender checks the logging messages for the appropriate output.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3393 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 15:12:48 +00:00
017ab6b690
Experimental versions of downsampler and Ryan's deduper are now available either
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as walker attributes or from the command-line. Not ready yet! Downsampling/deduping
works in a general sense, but this approach has not been completely optimized or validated.
Use with caution.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3392 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 05:40:05 +00:00
46ba88018d
Updated to the new readHeader(..) api
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3391 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 04:06:34 +00:00
d65b2d32d1
Removed AnnotatorROD which has been ported to Tribble
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3387 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 03:39:34 +00:00
b82116f488
Removed AnnotatorROD which has been ported to Tribble
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3386 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 03:39:20 +00:00
6b96f025f5
Tribble integration for indexing the AnnotatorInputTable format
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3385 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 03:37:54 +00:00
aedb9f6734
Bring SAMPileupCodec into compliance with new interface.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3383 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 01:23:29 +00:00
7cfb9ff3dc
updates for Tribble 82, fixes for Ryans case where multiple processes would attempt to read/write to the same index, and a couple other Tribble-centric bug fixes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3382 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-18 19:34:45 +00:00
635f61c22d
Clone the other guy too
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3381 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-18 18:56:01 +00:00
eb200e4cce
Hrumph. Don't just add pointers to the same objects, actually clone the underlying arrays.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3379 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-18 17:13:44 +00:00
e016491a3d
Major refactoring of Depth of Coverage to allow for more extensible partitions of data (now can do read group, sample, and library; in any combination; adding more is fairly easy). Changed the by-gene code to use clones of stats objects, rather than munging the interval DoCs. (Fix for Avinash. Who, hilariously, thinks my name is Carl.) Added sorting methods to ensure static ordering of header and body fields.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3377 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-18 16:58:13 +00:00
68719615be
For multiple matches, shifted counter to be 1-based
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3370 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-18 02:41:50 +00:00
73e2e32837
Fix typo.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3369 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-17 21:04:00 +00:00
ebd0fabf86
First pass updates to annotations to work with indels. HomopolymerRun indel behavior is currently turned off by a global boolean until it's ready to go live.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3368 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-17 21:02:13 +00:00
0791beab8f
Checking in downsampling iterator alongside LocusIteratorByState, and removing
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the reference implementation. Also implemented a heap size monitor that can
be used to programmatically report the current heap size.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3367 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-17 21:00:44 +00:00
b7d21627ab
Changes to DepthOfCoverage (JIRA items) and added back an integration test to cover it. Alterations to the design file generator to output all transcripts (rather than choosing one at random).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3366 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-17 17:23:00 +00:00
32389dc0a9
Fixed GQ estimate when chosen genotype isn't the most likely according to the GLs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3362 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-14 19:17:46 +00:00
3e9ad4bbd0
Porting SAM pileup ROD to Tribble as a case study.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3356 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-13 00:22:59 +00:00
6839c194cb
although holding on to memories can be fun, it's bound to hurt performance.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3355 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-12 19:26:58 +00:00
cac98ba5ef
a couple of small documentation fixes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3353 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-12 17:40:27 +00:00
3f07611187
Added support for -nSamples to varianteval (and getNSamplesForEval function). Allows you to calculate AC based metrics for files without genotypes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3350 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-12 13:36:31 +00:00
2c55ac1374
fixes for parallel processing problems with Tribble, a small bug in the resource pool, and some more documentation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3349 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-12 06:13:26 +00:00
6868ce988f
Fix hanging bug reported by Susanne Pfeifer (tiffy @ get satisfaction) where, if the last read(s) in a shard all have an
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indel in roughly the same location and that indel isn't covered by any other reads, LocusIteratorByState goes into an infinite
loop.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3348 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-11 17:31:19 +00:00
572b383fe2
Make VA annotate dbsnp again
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3345 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-11 14:06:53 +00:00
b09e7231d1
A quick implementation of the experimental covariates for the TGen folks to work with.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3344 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-11 01:08:52 +00:00
ec543b7b62
The Complete Genomics confusion matrix rates.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3338 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-10 14:52:10 +00:00
a51bd57566
First version of the smart batch merging tool.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3333 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-10 02:18:48 +00:00
76efa757f0
Switched over to reviewed version of Picard patch. In process, did some optimization to the IntervalSharder
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which improved startup time 5-10x when dynamically merging many BAMs.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3331 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-08 14:12:22 +00:00
64ccaa4c6a
Walkers and integration tests that calculate and compare callable bases
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3328 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-07 21:33:47 +00:00
d070554329
A walker that calculates read lengths, number and size of clipping events
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3327 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-07 21:32:51 +00:00
1749a49042
Mapping and base quality thresholds for DoC default to none
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3326 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-07 18:08:13 +00:00
7d2df3f511
example windowed ROD walker for Kristian, and updates to Tribble
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3325 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-07 17:12:50 +00:00
44de92e09d
Checking in the liftover script. I am including a post-processing walker to filter out bad records written in under 10 minutes as per my agreement with Mark.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3321 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-07 12:31:56 +00:00
18f1d31a22
Moving to and organizing in core.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3320 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-07 04:05:36 +00:00
4e0019b04f
Repair code that sorts and merges intervals.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3317 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-06 22:37:25 +00:00
72e030a670
require that snps be biallelic before we pass them to the TiTv calculation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3316 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-06 22:33:00 +00:00
7cecec7d00
Removing zero no-calls restriction in AC stats
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3314 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-06 18:55:07 +00:00
0e58fb7cc0
Moved over to be a walker inside the GATK
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3313 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-06 18:28:03 +00:00
78409dca0d
turned off the progress output from tribble when making an index, and fixing a case where the index file isn't writable so we instead make the index in memory.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3312 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-06 16:36:58 +00:00
5df0361bd2
trivial removal of unnecessary comments
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3309 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-06 03:51:14 +00:00
a0d71540df
speed-up for VCF, adding code to the VCF reader to automagically make an index if one doesn't already exist, and a change to the VCF writer unit test
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3305 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 20:19:42 +00:00
6bbcc47b5d
removing some out-of-date RODs and some unused genotype writer formats
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3304 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 19:07:13 +00:00
c998c48a23
adding code to detect out-of-date index files, which we now remove and regenerate if the target file is newer than the index file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3303 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 17:55:36 +00:00
a68f3b2e9c
VCF moved over to tribble.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3302 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 17:28:48 +00:00
0338345bee
Fixing the issue with reads having insertion immediately followed by a S/H cigar element causing out of window error.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3300 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 15:42:27 +00:00
f75e54e3f7
fixes for new package names in tribble 74
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3298 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 05:47:04 +00:00
354262eabe
New convenience methods to rodRefSeq for dealing with intervals that may be a superset of multiple exons. Needed for next commit.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3295 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 02:54:18 +00:00
03bea70f3a
Fixed edge case bug in cleaner: when no -L argument is used and a target interval abuts the end of the reference genome, we'll NullPointer at the first unmapped read.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3293 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-04 16:49:21 +00:00
f497213933
DbSNP moved over to tribble
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3288 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-03 06:02:35 +00:00
9dff578706
Added PG tag to bam header to let people know it's been cleaned.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3284 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 17:30:30 +00:00
0e10359a5e
Okay, finished up the ability to cap a base's qual by its read's mapping quality.
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This is experimental - I have not tested its performance on SNP calling, or even played around with it. If you want to test it out, go nuts. But don't come running to me if your results are not good.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3282 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 16:58:30 +00:00
850f36aa61
Changes to the Unified Genotyper's arguments:
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1. User can specify 4 confidence thresholds: for calling vs. emitting and at standard vs. 'trigger' sites.
2. User can cap the base quality by the read's mapping quality (not done yet).
3. Default confidence threshold is now Q30.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3281 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 16:44:24 +00:00
8bb15ef812
Checking in the reference implementation of the downsampler for back comparison.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3278 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 15:41:13 +00:00
1714c322c2
Reorg of UG args; checking in first before upcoming changes that will break integration tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3274 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 14:48:46 +00:00
cbed0b1ade
Adding GeliText tribble track as the first enabled Tribble track. This mean 'Variants' is no longer valid for a ROD type, use GeliText instead. I've updated all the references in the codebase.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3271 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-29 22:50:17 +00:00
82818a417b
Allow header fields to come in any order...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3269 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-29 18:33:10 +00:00
4617abf1ff
Fix bug in the interval sharder in cases where contigs specified in intervals are not present in any supplied BAM file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3268 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-28 20:42:04 +00:00
e2ff4167af
Added "#Family ID" as a possible header value for PlinkRod ... since that's in the new sequenom headers for pilot 3 validation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3266 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-28 18:38:33 +00:00
5dce16a8f1
Better genotype concordance module. Code refactoring for clarity (please see below/after for educational purposes). Now reports variant sensitivity, concordance, and genotype error rate by default. Also aggregates this data across all samples, so you get a per sample and overall stats for each of these in the allSamples row.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3265 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-28 13:10:11 +00:00
d9bf441391
Have UG emit calls at sites from one or more 'trigger' tracks when provided
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3257 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-26 05:04:43 +00:00
8f2bfac7a6
Bug fix for NullPointerException
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3256 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-26 05:02:09 +00:00
f5a3b128c8
Fixing bug that's not caught by integration tests:
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If the first eval seen has one or more no-calls, then that's the 2N chromosome count that gets set as the max for the metrics. Instead, just check that any eval's no-call count is 0.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3255 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-26 02:40:34 +00:00
29ab59a7b3
Bug fix for Kiran; insertions now get a null reference allele even if the ref input object is null
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3254 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-24 21:31:03 +00:00
c8d09a29ed
some quick changes to the VE output system - more to come.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3253 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 21:55:08 +00:00
7f4d5d9973
Ti/Tv by AC
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3252 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 17:56:29 +00:00
42bcca1010
Pulling out the left-alignment code for indels so that other walkers can use it.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3251 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 16:12:34 +00:00
e7c0ded40e
Fixed long-standing bug in GenotypeConcordance module of VariantEval which caused incorrect numbers to be displayed in the concordance table. The format of the concordance table has changed. Added a concordance summary table which gives overall genotype concordance summary stats by sample. None of the VE integration tests contained genotype information so I added a comp track with genotypes to one of the tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3247 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 15:48:41 +00:00
e0b51d0df0
Trigger cleaning of duplicate reads. Also beeter debug output.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3246 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 15:12:28 +00:00
3adf7fbf64
bug fix for known-indels used as consenses
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3245 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 13:52:51 +00:00
536f22f3bd
adding VC adaptor for GELI, along with unit tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3243 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 05:28:39 +00:00
8c94df6f00
Bug fix for Chris: deal with sites that have "semi-deletions"
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3241 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-22 18:34:41 +00:00
20379c3f82
Added location-caching optimization, temporary attributes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3236 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-22 11:35:45 +00:00
84ebceb9a6
Fix for Chris: need to use the appropriate conversion method. Added a warning to the adaptor.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3235 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-22 02:05:10 +00:00
ef6d900eb8
for now, set log error to -1
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3231 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 19:21:06 +00:00
e9e844fbf5
1. Reverting: dbsnp automatically is a comp
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2. Fixing logic for min Qscore calculation
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3230 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 18:51:35 +00:00
1373fee278
Because of the ugly VCF format, generic addCall() method of GenotypeWriter interface acquired an additional parameter, explicitly specified reference base (in VCF it's the base immediately *before* the event in case of indels, so we got to pass it). All implementing classes are modified to accomodate the change.
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VCFGenotypeWriterAdapter now explicitly uses the passed reference base instead of deriving it from VatriantContext (in SNP mode as well!), other writers simply ignore that additional argument.
SimpleIndelCalculationModel now WORKS (or rather, it does produce calls :) )
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3228 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 18:19:03 +00:00
ab34397d2e
Continuing to stamp out the non-ASCII copyright virus.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3227 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 14:50:45 +00:00
2fdc1cf490
Bed ROD track support
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3225 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 13:22:42 +00:00
51b3998082
deleting unused code from VariationFiltration
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3224 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 13:22:19 +00:00
4abd3b0b7b
Fixing known/novel calc now that dbsnp isn't a default comp track
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3223 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 05:43:59 +00:00
114819d980
Allow user to set min confidence score for comp tracks too
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3222 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 05:09:09 +00:00
3db73e0791
Renaming for consistency
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3221 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 03:00:43 +00:00
3b5673d967
1. Removed -all; by default all modules are used; use -none for no modules.
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2. Don't make dbsnp track be a comp by default (to cut back on output). Please let me know if someone wants this back for some reason.
3. Cleaned up dbsnp module output to print the right numbers.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3220 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 02:46:42 +00:00
hanna
delangel
chartl
depristo
aaron
weisburd
ebanks
rpoplin
kiran
asivache