bc64d4240f
Licensing update -- batch #2
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- caught all scala files that didn't have proper package information / class names
- included all source files in archive as well
GSATDG-5
2013-01-11 13:38:11 -05:00
4ea2c5df43
Updating updateAllLicenses scripts to include archived files
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GSATDG-5
2013-01-11 13:38:05 -05:00
28235f57f2
Adding package information to scala scripts that were missing it. Including archived ones.
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GSATDG-5
2013-01-11 13:38:05 -05:00
cc9a2aaee7
Script to identify code without package info
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- package information is critical for the licensing scripts. All java and scala files MUST contain package information.
GSATDG-5
2013-01-11 13:38:05 -05:00
85baf71b39
Merged bug fix from Stable into Unstable
2013-01-11 11:05:27 -05:00
d78539774f
Another RR bug: off by one error led to ArrayIndexOutOfBoundsException when working with multiple samples and the variant region ended 1 base after the end of the last read for a given sample.
2013-01-11 11:05:09 -05:00
79b93f659c
Merged bug fix from Stable into Unstable
2013-01-11 09:20:13 -05:00
67fafbb625
Forgot an include
2013-01-11 09:19:46 -05:00
6bf0cc32f9
When reducing multiple samples it is possible to try to close a region that for a given sample has no reads. Currently we'd NPE. Fixed.
2013-01-11 09:16:19 -05:00
e7906713d9
Moving some random walkers back to public as requested by Mark. Mauricio will the licenses get updated automatically?
2013-01-11 02:03:43 -05:00
3a51823c2a
Clean up imports
2013-01-10 23:35:01 -05:00
e4b7b1955c
Forgot to add the note about length normalization to the QD docs
2013-01-10 23:34:06 -05:00
ff5ac986d8
Fix docs for QD
2013-01-10 23:31:46 -05:00
352cb831d0
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
2013-01-10 21:27:06 -05:00
fac0bce916
add RunCoveredByNSamplesSites; changes in CoveredByNSamplesSites so it can work in parallel; also, move it to diagnostics
2013-01-10 21:26:49 -05:00
ea8c8573d2
Fixing ParseLicense script for scala syntax
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- Scala allows package objects in its syntax, so the script needs to be aware of that and not add "*/" every time it sees it.
GSATDG-5
2013-01-10 18:24:24 -05:00
e5913e50b2
Updating licenses for all scala files
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GSATDG-5
2013-01-10 17:46:10 -05:00
9b45e54ae6
Adding package information to stray scala files
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GSATDG-5
2013-01-10 17:45:36 -05:00
6623148838
Removing CMI scripts from the GATK repo
2013-01-10 17:45:36 -05:00
2a4ccfe6fd
Updated all JAVA file licenses accordingly
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GSATDG-5
2013-01-10 17:06:41 -05:00
75a0d0b193
Cleaning CRLF terminations in the licenses
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- made all unix style line endings
- removed private license since it was similar to protected license. Made it a symlink.
GSATDG-5
2013-01-10 17:06:29 -05:00
dd177b1714
Removing fully commented out varianteval evaluators
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- Files were completely commmented out, and were screwing up my license script. Dont like them. Removed them.
GSATDG-5
2013-01-10 17:06:12 -05:00
5222f9c397
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
2013-01-10 14:40:16 -05:00
b109b124bd
Remove non-ASCII chars
2013-01-10 14:39:56 -05:00
535c4c0d34
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
2013-01-10 14:39:34 -05:00
1b535f6d91
I'd like to put these under version control just to be safe. They are components of the LD-corrected PCA/VarianceComponent tool in private/python
2013-01-10 14:37:27 -05:00
1e083b2388
private/protected licenses updated to the version from legal; public should be the old GATK license.
2013-01-10 14:37:07 -05:00
80dec72c53
Merge branch 'master' of gsa2:/humgen/gsa-scr1/chartl/dev/unstable
2013-01-10 14:35:59 -05:00
31a5f88c4f
Expanded unit tests to cover the Concordance Metrics class fairly uniformly.
2013-01-10 14:33:47 -05:00
f801cb3be5
Updating Queue maven version to 0.0.2
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- After changes to the repositories, we are making sure that cmi-queueext is getting the right file.
2013-01-10 13:46:49 -05:00
3e52ce5fa8
Remove DepthOfCoverage.java because it is no longer public
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- Move Pileup.java and PrintReads.java to their new homes
2013-01-10 11:45:38 -05:00
4a8466783a
License Parser and update all license scripts
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* Implemented a script that parses and replaces the license (to be used by git on every commit)
* Implemented a shell script that makes use of the license parser to add the license to all java files in the repo
GSA-685 GSATDG-6 GSATDG-16
2013-01-09 15:56:50 -05:00
1a18947abf
Adding new command line argument requested on the forum to control the maximum number of haplotypes that are sent forward for genotyping. In the presence of a large degree of heterozygosity the current algorithm breaks down and so this argument would need to be increased.
2013-01-09 15:54:02 -05:00
487fb2afb4
Bug fix for the case of overlapping assembled and partially-assembled events created by the HC. Unfortunately the symbolic allele can't be combined with the indel allele because the reference basis will change.
2013-01-09 15:30:46 -05:00
6787f86803
Eliminate the import of DiploidGenotype, which switched public/private underneath me but for some reason didn't stop me from compiling...
2013-01-09 13:23:24 -05:00
c1de92b511
Add in some todo items
2013-01-09 13:16:06 -05:00
8d126161e2
Merge branch 'master' of gsa2:/humgen/gsa-scr1/chartl/dev/unstable
2013-01-09 13:15:04 -05:00
3a0dd4b175
Oops, I broke the build. NOW we shouldn't have any more public->protected dependancies.
2013-01-09 11:12:28 -05:00
a921b06e02
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
2013-01-09 11:06:17 -05:00
4fa439d89e
Move some classes back to public because they are used in the engine. Move some test classes to protected. We should have no more public->protected dependancies now
2013-01-09 11:06:10 -05:00
396bce1f28
Reverting this change until we can figure out the right thing to do here.
2013-01-09 10:51:30 -05:00
676e79542a
Bring CombineVariants back to public since it's used for SG. I needed to break ChromosomeCountConstants out of ChromosomeCounts to make this work.
2013-01-09 10:39:48 -05:00
c87ad8c0ef
Bug fixes related to HC's GGA mode. Tracking just the artificial allele isn't sufficient when there are multiple GGA records that change the reference basis. Also, duplicated records screw up the tracking of merged alleles.
2013-01-09 10:00:46 -05:00
ad7c2a08d4
Normalize by the event type counts, not the total genotype counts: more useful normalization.
2013-01-09 09:12:41 -05:00
b56754606b
Initial break-out of GenotypeConcordance as a standalone walker. Some basic functionality testing. Currently performs only a pairwise comparison, but is very careful about proper tabulation through the GenotypeType enum.
2013-01-09 00:34:07 -05:00
15ca5015cd
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
2013-01-08 21:53:36 -05:00
d6071728e8
add new walker to find sites with good coverage
2013-01-08 17:10:38 -05:00
264cc9e78d
Resolve protected->public dependencies for BQSR by wrapping the BQSR-specific arguments in a new class.
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Instead of the GATK Engine creating a new BaseRecalibrator (not clean), it just keeps track of the arguments (clean).
There are still some dependency issues, but it looks like they are related to Ami's code. Need to look into it further.
2013-01-08 16:23:29 -05:00
ee7d85c6e6
Move around the DiploidGenotype classes (so it can be used by the GATKPaperGenotyper)
2013-01-08 15:53:11 -05:00
0e2e672521
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
2013-01-08 15:46:39 -05:00
Mauricio Carneiro
Eric Banks
Ami Levy-Moonshine
Chris Hartl
Chris Hartl
Joel Thibault
Ryan Poplin