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
aafe9e6ca7
Try again to suppress hom genotypes
2011-07-21 02:15:44 -04:00
77e10a3280
Merge branch 'laptop'
2011-07-21 02:11:02 -04:00
e5c50fb3de
Suppress matching hom genotypes
2011-07-21 02:10:15 -04:00
50ab8c513b
Merge branch 'laptop'
2011-07-21 02:00:56 -04:00
ba4b1ce171
Even more formatting changes, trying to get the haplotypes to line up nicely
2011-07-21 02:00:34 -04:00
7770ddf2d6
Merge branch 'laptop'
2011-07-21 01:56:44 -04:00
5d21f7fa91
Don't show reference allele status
2011-07-21 01:56:39 -04:00
7695eb753d
More formatting
2011-07-21 01:53:36 -04:00
98444cbebb
Merge branch 'laptop'
2011-07-21 01:47:01 -04:00
dcd7d97b60
Formatting.
2011-07-21 01:46:38 -04:00
e2d0a2c459
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-21 01:42:50 -04:00
6cf26d8e7f
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/kiran/repositories/Sting-Unstable
2011-07-21 01:40:56 -04:00
e5b61eb9a0
Walker to compare RBP and Beagle haplotypes
2011-07-21 01:40:25 -04:00
6fa17d86ae
Completely hacked together version of a FreeMarker + javadoc + custom doclet walker documentation generator
2011-07-21 00:18:07 -04:00
32730b1832
Fixed md5 due to new PL ordering
2011-07-20 22:17:15 -04:00
45c73ff0e5
Runs and emits an HTML document
2011-07-20 17:16:33 -04:00
d31b176e15
Removed GATK use of distributed parallelism framework.
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Moved distributed GATK prototype code into distributedutils, separating from threading package
2011-07-20 16:26:09 -04:00
4b0b7f4b32
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-20 14:49:25 -04:00
Mark DePristo
Guillermo del Angel
Christopher Hartl
Matt Hanna
Kiran V Garimella