2d5bbecd9e
Merged bug fix from Stable into Unstable
2011-08-16 14:19:04 -04:00
9d4add3268
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-08-16 14:18:03 -04:00
170d1ff7b6
Fix in UG for trying to call indels at IUPAC code bases when in EMIT_ALL_SITES mode
2011-08-16 14:17:46 -04:00
9f3328db53
fixing read group name collision: before writing the read into respective stream in nway-out mode we now retrieve the original rg, not the merged/modified one
2011-08-16 13:45:40 -04:00
ab0b56ed11
Minor doc fixes
2011-08-16 12:55:45 -04:00
125ad0bcfa
Added docs to RTC
2011-08-16 12:46:48 -04:00
ef9216011e
Added docs to IR
2011-08-16 12:24:53 -04:00
ab1e3d6a98
Use the right set of sample names
2011-08-16 01:03:05 -04:00
36c7f83208
Refactoring VE stratifications so that they don't pass around bulky data; instead just pull needed data from the VE parent. This allows us stop using deprecated features of the rod system.
2011-08-15 16:31:57 -04:00
1246b89049
Forgot to initialize variants on the merge
2011-08-15 16:00:43 -04:00
045e8a045e
Updating random walkers to new rod system; removing unused GenotypeAndValidateWalker
2011-08-15 14:05:23 -04:00
fc2c21433b
Updating random walkers to new rod system
2011-08-15 13:29:31 -04:00
3d56bbf087
Resolving merge conflicts
2011-08-15 12:28:05 -04:00
9ddbfdcb9f
Check filtered status before applying to alt reference
2011-08-15 12:25:23 -04:00
c7b69a4574
Fixed integration tests
2011-08-14 16:38:20 -04:00
6ae3f9e322
Wrapped clipping op information
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The clipping op extra information being kept by this walker was specific to the walker, not to the read clipper. Created a wrapper ReadClipperWithData class that keeps the extra information and leaves the ReadClipper slim.
(this is a quick commit to unbreak the build, performing integration tests and will make further commits if necessary)
2011-08-14 15:44:48 -04:00
8a51732049
Fixes to ReadClipper and added Reference Coordinate clipping.
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* Added reference coordinate based hard clipping functions. This allows you to set a hard cut on where you need the read to be trimmed despite indels.
* soft clipping was messing up cigar string if there was already a hard clip at the beginning of the read. Fixed.
* hard clipping now works with previously hard clipped reads.
2011-08-14 14:54:33 -04:00
291d8c7596
Fixed HardClipping and Interval containment
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* Hard clipping was wrongfully hard clipping unmapped reads while soft clipping then hard clipping mapped reads. Now we throw exception if we try to hard/soft clip unmapped reads and use the soft->hard clip procedure fore every mapped read.
* Interval containment needed a <= and >= to make sure it caught the borders right.
2011-08-14 14:54:33 -04:00
0be1dacddb
Refactored interval clipping utility
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reads are clipped in map() and now we cover almost all cases. Left behind the case where the read stretches through two intervals. This will need special treatment later.
2011-08-14 14:54:33 -04:00
9d2cda3d41
Removed a public -> private dependency in our test suite.
2011-08-12 17:29:10 -04:00
bb4ced3201
SnpEff-related fixes.
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-To correctly handle indels and MNPs, only consider features that start at the current locus,
rather than features that span the current locus, when selecting the most significant effect.
-Throw a UserException when a SnpEff rodbinding is not provided instead of simply not adding
any annotations and silently returning.
2011-08-12 15:26:24 -04:00
10e873d9c6
Merge branch 'repval'
2011-08-12 15:24:31 -04:00
31dc831531
Merged bug fix from Stable into Unstable
2011-08-12 13:26:41 -04:00
9121b8ed65
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-12 12:24:19 -04:00
7ed120361d
Fixed bug that required symbolic alleles to be padded with reference base and added integration test to test parsing and output of symbolic alleles
2011-08-12 12:23:44 -04:00
7ea9196321
Better error message for name/type clashes.
2011-08-12 11:18:14 -04:00
27f0748b33
Renaming the HapMap codec and feature to RawHapMap so that we don't get esoteric errors when trying to bind a rod with the name 'hapmap' (since it was also a feature).
2011-08-12 11:11:56 -04:00
005bd71be3
Working too quickly earlier. Fixing syntax.
2011-08-12 10:29:36 -04:00
c7ca33cbff
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-12 10:12:09 -04:00
639a01f382
Updating integration test now that VE has been updated
2011-08-12 07:15:08 -04:00
41f3da75d7
Implementation in VE was confusing 'variant' status vs. 'polymorphic' status. This led to issues because we now match types of eval and comp; specifically, subsetting a VC to a monomorphic sample can't change the 'variant' status of the VC (it's still a variant site or otherwise we'll never match the comps, which breaks GenotypeConcordance). CountVariants really got this wrong. Fixed. VE now passes all integration tests.
2011-08-12 02:22:44 -04:00
45f973ab1f
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-12 00:40:18 -04:00
eba316621d
Finish moving VE over to new rod system and fixing up the type inconsistency between eval and comp rods. Now the novel count is always 0 under the known stratification. :)
2011-08-12 00:40:08 -04:00
9de06560df
Update to new RodBinding system
2011-08-11 17:54:16 -04:00
f1d1252be2
Fixing syntax of BQSR and UG performance tests.
2011-08-11 17:04:09 -04:00
902eb0c61e
Adding dbsnp annotation back into the UG integration tests
2011-08-11 13:55:03 -04:00
90771b74b4
When matching eval to comps, try to choose the one with the same alt allele.
2011-08-11 13:55:01 -04:00
200f73b008
No reason to warn the user anymore because it's no longer possible for them to specify a dbsnp file on the command-line.
2011-08-11 13:44:07 -04:00
e93538cdf7
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-11 13:39:36 -04:00
265c3d744b
Fixing VariantEval logic and having it use the new rod system.
2011-08-11 13:39:34 -04:00
b705d9cf15
Oops, these VariantAnnotator input bindings aren't needed during the UG
2011-08-11 13:17:16 -04:00
7fade88070
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-11 11:02:47 -04:00
c7b9a9ef0a
Updating UnifiedGenotyper to use the new rod binding system.
2011-08-11 11:02:11 -04:00
418a4d541f
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-11 11:01:38 -04:00
e71255d3c2
GATKDocsExample walker
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-- Shows the best practice for documentating a walker with the GATKdocs
-- See http://www.broadinstitute.org/gsa/wiki/index.php/GATKdocs#Writing_GATKdocs_for_your_walkers for a brief discussion
2011-08-11 11:01:21 -04:00
79c86e211f
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-11 09:59:20 -04:00
ea42ee4a95
Updating BQSR for the new rod binding system.
2011-08-11 09:58:42 -04:00
8cdc0cbd9c
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-11 08:58:49 -04:00
40e06f9afb
Fixed broken RodBinding defaults.
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-- Verified now to be correct at runtime
-- UnitTest covers this
-- createTypeDefault now takes a Type, not a Class, so that parameterized classes can have their parameter fetched in the defaults.
2011-08-11 08:58:30 -04:00
dd5fe8291d
Fixing up some comments in the BQSR
2011-08-11 08:36:00 -04:00
Ryan Poplin
Andrey Sivachenko
Eric Banks
Mauricio Carneiro
David Roazen
Guillermo del Angel
Menachem Fromer
Mark DePristo