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
e1b9cf2595
getting rid of useless imports
2011-07-21 21:48:05 -04:00
eb104156ae
now takes -sp (number of samples per pool) instead of estimating the maxAlleleCount from the total number of samples in the file (this was only good for test runs).
2011-07-21 21:45:20 -04:00
8d7ef1bb51
Complete refactor of the ReplicationValidation framework, plus the following new functionality:
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* merges all pools in a lane.
* merges all lanes in a site.
2011-07-21 21:39:00 -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
6f095a7752
Merge branch 'laptop'
2011-07-21 03:17:14 -04:00
c40b0fe1a3
Only evaluate genotypes that have a PQ field
2011-07-21 03:16:57 -04:00
11e498979f
Merge branch 'laptop'
2011-07-21 03:13:56 -04:00
593787c1d0
Only evaluate genotypes that have a PQ field
2011-07-21 03:12:50 -04:00
f01fc732f4
Merge branch 'laptop'
2011-07-21 03:04:30 -04:00
8d7b7e259e
Track number of genotypes with PQ field
2011-07-21 03:04:09 -04:00
d8f5bbeefc
Merge branch 'laptop'
2011-07-21 03:02:06 -04:00
67031de95c
Formatting changes
2011-07-21 03:01:53 -04:00
c135d8832c
Merge branch 'laptop'
2011-07-21 02:59:46 -04:00
bfecc60fd6
Formatting changes
2011-07-21 02:59:32 -04:00
a687f04615
Merge branch 'laptop'
2011-07-21 02:51:37 -04:00
620a4e5aed
Handle missing PQ fields
2011-07-21 02:51:29 -04:00
82a0e67219
Merge branch 'laptop'
2011-07-21 02:46:59 -04:00
c8d381f51e
Formatting fixes for haplotype metrics
2011-07-21 02:46:43 -04:00
1992973e05
Merge branch 'laptop'
2011-07-21 02:43:19 -04:00
3cde209632
Print haplotype metrics
2011-07-21 02:42:58 -04:00
de239d8f44
Merge branch 'laptop'
2011-07-21 02:16:14 -04:00
Kiran V Garimella
Guillermo del Angel
Mark DePristo
Khalid Shakir
Mauricio Carneiro
Christopher Hartl
Matt Hanna