Mark DePristo
|
51b0dd01c3
|
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
|
2011-07-18 10:47:29 -04:00 |
|
Mark DePristo
|
6f26c07b85
|
Removed the SpecificDifference class. Now Difference classes always have the option to remember specific master and test values. This means that all summarized differences carry with them specific examples of their differences. Consequently, now even summarized differences give at least one example of the specific difference, even when the count of the difference is > 1. Unit tests updated. Added DiffObjects integrationtest. VCFDiffableReader now specifically reads the first line of the VCF file to capture the version number.
|
2011-07-18 10:42:35 -04:00 |
Kiran V Garimella
|
b2b7d27fed
|
Merge branch 'laptop'
|
2011-07-18 00:25:46 -04:00 |
|
Kiran V Garimella
|
497721a799
|
Added class documentation string.
|
2011-07-18 00:25:21 -04:00 |
|
Kiran V Garimella
|
ac9c66138d
|
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
|
2011-07-18 00:20:33 -04:00 |
|
Kiran V Garimella
|
8167aba601
|
Moved (poorly named) MergeAndMatchHaplotypes to public. Added integration test
|
2011-07-17 22:47:32 -04:00 |
|
Mark DePristo
|
9992c373be
|
Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes.
|
2011-07-17 20:29:58 -04:00 |
|
Kiran V Garimella
|
4ea433f8e1
|
Moved PhaseByTransmission to public
|
2011-07-17 19:42:00 -04:00 |
|
Mark DePristo
|
4db2b13e9e
|
Rev tribble.
Just added more documentation for diffEngine and pointer to new wiki:
http://www.broadinstitute.org/gsa/wiki/index.php/DiffEngine
|
2011-07-17 13:05:04 -04:00 |
|
Mark DePristo
|
92a1c0c278
|
Moved the varianteval/tags/DataPoint.java and varianteval/tags/Analysis.java to varianteval/utils. This allows rsync to see these files with the -C option, as tags is some kind of reserved CVS keyword.
|
2011-07-17 10:14:23 -04:00 |
Menachem Fromer
|
72f4cf9c0e
|
Walker to perform deterministic annotation of phasing by transmission (to be compatible with RBP's definition of consecutive pairwise phasing)
|
2011-07-15 17:44:31 -04:00 |
|
Mark DePristo
|
5ffeddd3b1
|
better to use _ instead of ., as this is a special case later.
|
2011-07-14 14:45:16 -04:00 |
Eric Banks
|
ed6beae1f3
|
Adding headers to diffable reading for VCFs
|
2011-07-14 13:55:35 -04:00 |
|
Eric Banks
|
0c54c796ed
|
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
|
2011-07-13 14:57:33 -04:00 |
|
Eric Banks
|
6a431da554
|
Don't output source and ref header lines anymore. Short-term motivation for this is that I'd like this tool when run on a VCF to emit the exact same VCF. Long-term motivation is that these tags should be output by the VCF writer itself for all tools.
|
2011-07-13 14:40:01 -04:00 |
|
Menachem Fromer
|
74aa49e423
|
Merged bug fix from Stable into Unstable
|
2011-07-13 12:12:42 -04:00 |
|
Menachem Fromer
|
fa3ff53508
|
Filters should only be applied to the new VC if the old VC had filters applied
|
2011-07-13 11:58:16 -04:00 |
Ryan Poplin
|
837fb8f689
|
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
|
2011-07-12 15:39:26 -04:00 |
|
Ryan Poplin
|
5077c94d85
|
Adding MappingQualityUnavailableReadFilter to the SNP and indel CountCovariates
|
2011-07-12 15:39:07 -04:00 |
|
Mark DePristo
|
01fd6a6949
|
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
|
2011-07-12 15:20:44 -04:00 |
|
Mark DePristo
|
ccedd6ff4c
|
Difference is now the general form -- used to be SummarizedDifference. The old Difference class is now a subclass of Difference that includes pointers to specific the master and test DiffElements.
Added a size() function that calculates the number of elements tree from a DiffElement.
|
2011-07-12 15:20:28 -04:00 |
|
Eric Banks
|
a2597e7f00
|
This commit incorporates several different changes that each pretty much break all the VCF-based integration tests, so I bunched them all together. We now officially emit VCF4.1 files (woo hoo), which means that the VCF headers are now all different (header version is 4.1 plus counts for some of the annotations are 'A' or 'G'). Also, I've added a Read Filter for reads with MQ=255 ('unavailable' in the SAM spec) and have applied this to the UG and the RMS MQ annotation.
|
2011-07-12 14:11:53 -04:00 |
Guillermo del Angel
|
c4c145afb9
|
Merged bug fix from Stable into Unstable
|
2011-07-12 13:44:48 -04:00 |
|
Guillermo del Angel
|
cfe43e3971
|
Bug fix for Genotype given alleles: if we are in INDEL mode ignore SNPs and MNPs instead of emitting an empty site with alleles but no annotations
|
2011-07-12 13:43:46 -04:00 |
|
Mark DePristo
|
05212aea62
|
reader now takes an argument for the maximum number of elements to read from the file.
|
2011-07-12 08:53:19 -04:00 |
|
Mark DePristo
|
8056a3fe89
|
getElement() now uses O(1) get from hash instead of linear O(n) search. Enables us to read large files easily.
|
2011-07-12 08:52:31 -04:00 |
|
Eric Banks
|
d7d15019dd
|
Adding support for other simple header line types (e.g. ALT) and cleaning up the interface a bit.
|
2011-07-12 01:16:21 -04:00 |
|
Eric Banks
|
400b0d4422
|
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
|
2011-07-11 23:38:57 -04:00 |
|
Mark DePristo
|
893cc2e103
|
Making the package public, so there's no dependances from public -> private
|
2011-07-11 23:15:08 -04:00 |
|
Eric Banks
|
e3748675db
|
Support for VCF 4.1 header counts
|
2011-07-11 17:40:45 -04:00 |
|
Mark DePristo
|
bd29236684
|
Merge branch 'master' into diffengine
|
2011-07-08 14:08:17 -04:00 |
|
Ryan Poplin
|
2a4b3ae4a2
|
Cleaning up / removing most of the monkeying around with annotation values that happens in VariantDataManager
|
2011-07-08 12:48:33 -04:00 |
|
Mark DePristo
|
8add2a3866
|
Merge branch 'master' into diffengine
|
2011-07-08 09:15:54 -04:00 |
|
Mark DePristo
|
3d4f0e9dd7
|
Now supports the case where you have multiple AC values in the info field.
|
2011-07-07 17:21:15 -04:00 |
|
Ryan Poplin
|
212e9a1a0c
|
Fixing unstable build after stable commit
|
2011-07-07 15:18:57 -04:00 |
|
Ryan Poplin
|
11d9a0473a
|
Merged bug fix from Stable into Unstable
|
2011-07-07 15:03:58 -04:00 |
|
Ryan Poplin
|
50111db2b7
|
Fixing non-determinism in single-threaded VQSR by moving references to cern.Normal over to the static random generator available in GenomeAnalysisEngine
|
2011-07-07 15:02:48 -04:00 |
|
Eric Banks
|
52f6f9fdcc
|
Merged bug fix from Stable into Unstable
|
2011-07-06 16:05:48 -04:00 |
|
Eric Banks
|
54121eb082
|
Catch malformed bams that cause the writer to run in infinite loops
|
2011-07-06 16:05:08 -04:00 |
|
Ryan Poplin
|
bdef233d4d
|
Merged bug fix from Stable into Unstable
|
2011-07-06 10:05:02 -04:00 |
|
Ryan Poplin
|
e8ed6b7f0f
|
Adding more comments to main VQSR walker. Fixing copyright lines. Bug fix for default paths to now point to public/R/ instead of R/ Bug fix in VQSR for the path to the R scripts not ending in a slash.
|
2011-07-06 10:01:14 -04:00 |
|
Guillermo del Angel
|
8e8b901d12
|
Merged bug fix from Stable into Unstable
Merge branch 'master' into unstable
|
2011-07-06 09:57:55 -04:00 |
|
Guillermo del Angel
|
81a4d18468
|
Mark several indel-related arguments as @Hidden
|
2011-07-06 09:56:38 -04:00 |
|
Ryan Poplin
|
fb315b5f8c
|
Merge branch 'incoming'
|
2011-07-02 18:10:48 -04:00 |
|
Ryan Poplin
|
41d46059e7
|
fixing bad format statement
|
2011-07-02 18:09:17 -04:00 |
|
Ryan Poplin
|
3804afeb8a
|
Merge branch 'incoming'
|
2011-07-02 17:55:39 -04:00 |
|
Ryan Poplin
|
781c0c33a4
|
Use the worst X% of calls in addition to the bad training sites list. Don't include the already added calls in the calculation of X%
|
2011-07-02 17:55:10 -04:00 |
|
Ryan Poplin
|
6b8af6afd8
|
Merge branch 'master' of ssh://gsa1.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
|
2011-07-02 17:15:56 -04:00 |
|
Ryan Poplin
|
fdc2ebb321
|
Adding ability to specify in VQSR a list of bad sites to use when training the negative model. Just add bad=true to the list of rod tags for your bad sites track.
|
2011-07-02 17:15:13 -04:00 |
|
Guillermo del Angel
|
09af6bbc6c
|
Ugh - backed out experimental code not for public consumption unintendedly committed
|
2011-07-02 16:58:57 -04:00 |