1dba8b768c
Merge branch 'laptop'
2011-07-23 01:39:15 -04:00
57e3d136eb
Don't try to phase triple-hets either.
2011-07-23 01:38:58 -04:00
f366124778
Merge branch 'laptop'
2011-07-23 01:25:36 -04:00
45f2ca8d99
Changed MD5 to reflect latest changes to PhaseByTransmission.
2011-07-23 01:21:07 -04:00
5af9d50183
Merge branch 'laptop'
2011-07-23 01:12:06 -04:00
5521919cc9
Fixed bug where variants to phase were not being selected properly.
2011-07-23 01:11:28 -04:00
7da99388ac
Merge branch 'laptop'
2011-07-23 01:01:11 -04:00
58eed20b83
Copy all entries from the attributes map, rather than attempting to modify an unmodifiable map.
2011-07-23 01:00:46 -04:00
b5deff48e6
Merge branch 'laptop'
2011-07-23 00:56:50 -04:00
5638017137
Removed the nofilters argument specification in the integrationtest
2011-07-23 00:56:23 -04:00
ffa361f57f
Merge branch 'laptop'
2011-07-23 00:50:38 -04:00
9417ba8c2c
Modified to accept multi-sample VCFs, removed the application of filters, and changed transmission probability field to be a genotype field rather than an INFO field.
2011-07-23 00:48:26 -04:00
28b9432d26
Docs for read filters, the engine, and the UserExceptions.
2011-07-22 16:09:21 -04:00
051c1dc639
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-22 15:59:00 -04:00
d7b3f40259
Merge remote-tracking branch 'unstable/master'
2011-07-22 14:45:24 -04:00
4f78025b0b
Merged bug fix from Stable into Unstable
2011-07-22 14:42:04 -04:00
4080e2cd88
* Added the decoy reference to the bundle under the b37 resources.
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* Updated the -svn argument to -ver since we don't use svn anymore (also updated the wiki).
2011-07-22 14:41:22 -04:00
f0be7348be
Generalized handler to allow it to be used with any arbitrary class structure.
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DocumentedGATKFeature now includes a field for the group name.
Build.xml works with public / private now.
2011-07-22 14:07:40 -04:00
f50145b872
Reinitialize random seed in the bwa bindings from the fixed seed stored in the
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BWA support files every time the support files are loaded.
2011-07-22 13:41:53 -04:00
453954182e
Generalized the documentation system to use a class-specific annotation and processor.
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Need to generalize and bug fix the system. But at a high level it's working now.
2011-07-22 13:18:33 -04:00
b8a0fd2a8d
Multiply fractionRandom by 100.0 so that the line that indicates the percentage of variants that will be output says (for instance) 90%, not 0.9%
2011-07-22 11:54:59 -04:00
aab527064e
debug version
2011-07-22 10:32:56 -04:00
9e88d51db9
Removed now unused @version tags from walker docs.
2011-07-22 09:57:03 -04:00
88bbd9581a
debug version
2011-07-22 09:53:20 -04:00
1e80d715ff
debug version
2011-07-22 09:47:10 -04:00
421b70ca4f
Removed previous, and largely unused, help system extensions.
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This involved deleting the utils/help/*Taglet.java classes, which parsed out these fields unnecessarily
This also involved removing the few uses of these from the codebase. For these uses, though, almost all were an identical copy of the first line of the docs, which is the default javadoc behavior anyway.
2011-07-22 09:42:44 -04:00
9c1bd3b75a
debug version
2011-07-22 09:21:44 -04:00
172b35372b
Moved all of the distributed GATK code to archive.
2011-07-22 09:20:32 -04:00
e922ebc29d
Missed this template for walker index.
2011-07-22 09:13:33 -04:00
90b887372c
debug version
2011-07-22 09:03:33 -04:00
3d0853149b
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-22 08:13:58 -04:00
6afe63690d
Two more true oneoffs (committed mostly for didactic purposes): codec that reads Mills/Devine indel table into a vcf and another (in progress) that will read indel chip genotype data and produce a vcf
2011-07-22 08:13:05 -04:00
8b8f121cfb
Merge branch 'master' of ssh://gsa3.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-21 23:01:11 -04:00
59eb1f4663
Memory limits changed from Int to Double.
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Updated LSF calls to read memory units from config along with tweaks to select hosts.
Moved some common code from GridEngine and LSF to super classes.
2011-07-21 22:57:18 -04:00
81d0cab27e
Walker index html now emited.
2011-07-21 16:01:54 -04:00
e892489696
V2 of the document system.
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Now uses GATKDoc class to organize documentation for arguments.
Arguments now listed by feature (required, optional, hidden, etc) and link to detailed information about the argument in the html
Lots of code moving between Class and ClassDoc objects. Should be refactored into a single static utility class.
2011-07-21 15:20:34 -04:00
87f991aee7
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-21 13:35:24 -04:00
2f5d10d16b
Fix bug wherein aligner could be closed prior to its being used to lowercase sequences.
2011-07-21 13:21:48 -04:00
7054c5342f
When using the BWA bindings, you have to explicitly call close() to get the
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bindings to release memory.
It may or may not be possible to implicitly close triggered by the GC; I'll add a JIRA.
2011-07-21 12:13:29 -04:00
84c66d4b92
Bug fixes
2011-07-21 11:52:51 -04:00
c4684f4659
A true oneoff: walker that reads in vcf with multiallelic PL's in wrong ordering and flips them around to output in correct order
2011-07-21 11:20:46 -04:00
623143454b
Merge branch 'laptop'
2011-07-21 11:07:02 -04:00
bf6388fa8c
Print haplotype start locus
2011-07-21 11:06:45 -04:00
15610ce0c3
Per Matt's request, disabling BWA-based integration tests so he can assess bamboo memory usage.
2011-07-21 11:04:22 -04:00
1aefc02d2e
Merge branch 'laptop'
2011-07-21 10:54:15 -04:00
45e536dca8
Reenable haplotype printing
2011-07-21 10:40:40 -04:00
664246937c
Try to resolve merge conflict
2011-07-21 10:19:26 -04:00
1933be36b4
Ignore sites where the alleles don't match between the two files
2011-07-21 03:44:02 -04:00
d9909537ef
Merge branch 'laptop'
2011-07-21 03:22:59 -04:00
58873c391f
Don't print the haplotypes anymore - the metrics will do
2011-07-21 03:22:44 -04:00
Kiran V Garimella
Mark DePristo
Eric Banks
Mauricio Carneiro
Matt Hanna
Guillermo del Angel
Khalid Shakir
Christopher Hartl