2e5d38fd0e
Updating to latest google caliper code
2013-01-11 15:17:16 -05:00
b2990497e2
Refactor LIBS into utils.locusiterator before refactoring
2013-01-11 15:17:16 -05:00
e952296c10
Adding HC GGA integration test to cover duplicated input alleles.
2013-01-11 15:01:27 -05:00
7f7f40f851
Adding additional HC GGA integration tests to cover more complicated input alleles.
2013-01-11 14:36:21 -05:00
9ed922d562
Updating licenses to Eric's last commit
...
- for now we're still running the script by hand, soon automated solution will be in place.
GSATDG-5
2013-01-11 14:33:00 -05:00
009d2f5705
Removed CMI specific script from GATK repo
2013-01-11 14:33:00 -05:00
e9a8b1a403
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
2013-01-11 14:18:26 -05:00
9519c3fd6f
(1) add scala script to merge bam files; (2) few change in Queue script that run the new CoveredByNSamplesSites walker
2013-01-11 13:47:05 -05:00
bc64d4240f
Licensing update -- batch #2
...
- 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
...
GSATDG-5
2013-01-11 13:38:05 -05:00
28235f57f2
Adding package information to scala scripts that were missing it. Including archived ones.
...
GSATDG-5
2013-01-11 13:38:05 -05:00
cc9a2aaee7
Script to identify code without package info
...
- 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
...
- 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
...
GSATDG-5
2013-01-10 17:46:10 -05:00
9b45e54ae6
Adding package information to stray scala files
...
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
...
GSATDG-5
2013-01-10 17:06:41 -05:00
75a0d0b193
Cleaning CRLF terminations in the licenses
...
- 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
...
- 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
...
- 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
...
- 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
...
* 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
Mark DePristo
Ryan Poplin
Mauricio Carneiro
Ami Levy-Moonshine
Eric Banks
Chris Hartl
Chris Hartl
Joel Thibault