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
f32a32269c
minor change for eric
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3418 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-21 20:13:36 +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
355396109b
Bug fix to avoid build failure (class changed under me??)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3416 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-21 18:48:56 +00:00
1753d07b02
Added AnnotationByAlleleFrequencyWalker - walker takes an input vcf, a reference vcf and a list of annotations (with the -A argument). For each site present in both VCF's, it outputs the given annotations into the screen as well as allele frequency. Since HapMap vcf reference doesn't include AF in annotations, it computes it from Chromosome, Het and HomVar counts.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3415 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-21 18:31:34 +00:00
745d7c582f
added integration test for intervals with no coverage due to filtering
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3414 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-21 16:52:42 +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
7910a6a7cb
adding all of Tribble, not just select codecs, to the package
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3411 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-21 15:48:50 +00:00
d1098fa77b
Removing unnecessary dependences that were causing problems for Sendu
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3410 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-21 13:07:41 +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
fc57bccde8
trivial removal of directory
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3403 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-20 14:25:32 +00:00
a8f4ccf2f9
Retiring multi-sample genotyper
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3402 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-20 14:11:11 +00:00
1ab00e5895
Retiring multi-sample genotyper
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3401 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-20 14:10:56 +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
ffb1b46166
Added a GCCalculatorWalker for a oneoff analysis for Mark Daly (GC content of agilent 1.1 targets)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3395 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 18:49:51 +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
984c51efd3
Updated to use Tribble-based GATKFeature instead of TabularROD
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3390 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 03:42:12 +00:00
42ee16f256
Updated to use Tribble-based GATKFeature instead of TabularROD
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3389 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 03:41:37 +00:00
d8469e2fba
Updated to use Tribble-based GATKFeature instead of TabularROD
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3388 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 03:40:47 +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
2f3933148d
Added fast split(str, delimiter) methodf
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3384 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 03:37:26 +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
9e15299475
Misc cleanup in variant recalibrator.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3380 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-18 17:37:01 +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
886e9c1297
Now can take a VCF file as input
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3378 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-18 17:06:12 +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
2a212c497f
minor improvements and bug fixes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3376 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-18 15:54:42 +00:00
43544cfdf9
remote control of IGV to jump to any number of loci in a file and screenshot the locus to a file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3375 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-18 12:59:36 +00:00
3c022e4b0c
Improved command-line-arg validation at startup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3374 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-18 02:46:17 +00:00
04e14ef85a
Refactored so it could be used for knownGene and CCDS as well as refGene
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3373 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-18 02:45:11 +00:00
35b4bba35e
Refactored so it could be used for knownGene and CCDS as well as refGene
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3372 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-18 02:44:10 +00:00
bb86c0e03a
Improved error message
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3371 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-18 02:43:13 +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
delangel
depristo
hanna
chartl
aaron
weisburd
rpoplin