ff31fa7990
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-27 16:15:23 -04:00
5809a61b20
Merged bug fix from Stable into Unstable
2011-07-27 16:14:59 -04:00
64aad67b5f
Fixing dbSNP adaptor for complex indels (wasn)
2011-07-27 16:13:45 -04:00
20a3b31b61
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-26 19:29:45 -04:00
321afac4e8
Updates to the help layout.
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*New style.css, new template for the walker auto-generated html. Short description is no longer repeated in the long description of the walker.
*Updated DiffObjectsWalker and ContigStatsWalker as "reference" documented walkers.
2011-07-26 19:29:25 -04:00
405e521d44
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-26 17:56:48 -04:00
92a11ed8dc
Updated MD5 for PhaseByTransmissionIntegrationTest
2011-07-26 17:52:25 -04:00
412c466de6
Bug fix, wherein triple-hets after genotype refinement need to be left unphased, not just prior to refinement
2011-07-26 17:43:43 -04:00
81f8e05bfa
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-26 17:35:46 -04:00
f6a5e0e36a
Go for global integrationtest path first, if possible.
2011-07-26 17:35:30 -04:00
fec495e292
Fix a nasty little bug in the sharding system: if the last shard in contig n
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overlaps exactly on disk with the first shard in contig n+1, the shards
would be merged together to avoid duplicate extraction. Unfortunately,
the interval overlap filter couldn't handle shards spanning contigs, and
was choosing to filter out reads from contig n+1 which should have been
included.
I'm not completely sure why the BAM indexing code would ever specify that the
end of one chromosome had the same on-disk location as the start of the next
one. I suspect that this is a indexer performance bug.
2011-07-26 15:43:20 -04:00
088fc39308
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-25 15:54:56 -04:00
a53aeb75ab
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-25 15:10:35 -04:00
a29554e565
Removing the Genomic Annotator and its supporting classes
2011-07-25 15:10:25 -04:00
3afcb3415d
Max of 1000 records will be loaded and compared to avoid heap size problem.
2011-07-25 14:58:31 -04:00
8014fad6ff
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-25 13:20:44 -04:00
2ac490dbdf
Fix improper detection of command-line arguments with missing values.
2011-07-25 13:20:00 -04:00
90947ab359
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-25 12:53:56 -04:00
44bd9ae703
Restoring UninstantiableWalker, as it is not going to be possible to run ant test; ant gatkdocs without ant clean in between
2011-07-25 12:53:06 -04:00
acda8eb09c
Commented out test that causes new CommandLineGATK() to fail
2011-07-25 12:43:27 -04:00
357f503a21
Merge branch 'desktop'
2011-07-25 11:36:27 -04:00
0b43ee117c
Added the required=false tag to the -noST and -noEV arguments so the auto-help output doesn't look weird (i.e. listing arguments as required when their value has already been specified by default).
2011-07-25 11:35:34 -04:00
bbb8473f03
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-25 10:59:00 -04:00
1a268ff1fd
Refactor so that GenotypeAnnotation and InfoFieldAnnotation share common superclass VariantAnnotatorAnnotation
2011-07-25 10:55:09 -04:00
7f8e6a97ee
InfoFieldAnnotation now an abstract class extended by annotations so doc system works
2011-07-25 10:47:11 -04:00
4c6c16f895
Documented following the new gatkdoc framework
2011-07-25 00:25:08 -04:00
2039ce6102
Default values now displayed in arguments
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DiffEngine fixed so that newInstance() would work. Pretty quickly encountered a situation where newInstance() failed. Debug output now written when this occurs in the log.
Logger now used instead of standard out, with INFO the default level.
2011-07-24 22:56:55 -04:00
c43b5981f2
Hidden variables are hidden by default. Settable by command line option
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DiffObjectsWalker test arguments removed.
Minor refactoring of GATKDoclet
2011-07-24 20:52:44 -04:00
1c1f1da349
Fixing compilation
2011-07-24 20:01:59 -04:00
9f06f6c493
Split GATKDoclet from ResourceBundleDoclet. Refactored GaTKDocWorkUnit
2011-07-24 20:00:04 -04:00
ff85687679
Merge branch 'master' into help
2011-07-24 18:14:32 -04:00
83996f7951
Enumerated types are working.
2011-07-24 18:14:21 -04:00
3c34e9fa65
Cleanup emuns and tables
2011-07-24 17:45:58 -04:00
c620d96c96
Inline enum documentation is working
2011-07-24 17:22:14 -04:00
793e7d3d1d
Improved header and argument details
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Argument detail structure cleaned up. Only relevant pieces of information are shown now, and in a cleaner layout.
Misc. cleanup in the code.
2011-07-24 16:36:25 -04:00
c6af4efcdc
Implemented see also and version header
2011-07-24 16:10:17 -04:00
5e0fe2d0f9
Support for style.css via refactored common.html included in all files
2011-07-24 15:42:39 -04:00
d0ab6bf7a9
Now links to sub and superclass documentation, where possible.
2011-07-24 09:56:17 -04:00
e2dabb70b8
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-24 08:57:47 -04:00
1ef964c92c
Merge branch 'contig'
2011-07-24 02:40:42 -04:00
7ffedf211c
Contig comparator -- sorting contigs like Picard
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This is very useful if you want to output your text files or manipulate data in the usual chromosome ordering :
1
2
3
...
21
22
X
Y
GL???
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Just use this comparator in any SortedSet class constructor and your data will be sorted like in the BAM file.
2011-07-24 02:33:19 -04:00
6b501e267b
Includes non-concrete classes in docs
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CommandLineGATK has extraDocs to ReadFilter and UserException as well
2011-07-23 22:15:01 -04:00
7420ed098e
Semi-working version of extraDocs tag in annotation to refer to one capability being accessible in another
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Required a significant refactoring of the GATKDoclet, which now has a unified place where the ClassDoc, class, annotation, and handler are all stored together.
2011-07-23 22:07:30 -04:00
999acacfa1
Merge branch 'master' into help
2011-07-23 20:19:33 -04:00
1d3bcce2c4
Merge branch 'master' into NoDistributedGATK
2011-07-23 20:04:50 -04:00
e262f4e10b
gatkdoc now generalized to use @Annotation. Multiple subsystems now use annotation to receive docs
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Index expanded to use summary() annotation field
UserExceptions, ReadFilters, GATK engine all use the system to generate docs
Doclet expanded to handle lots of new cases
2011-07-23 20:00:35 -04:00
0b36b6540f
Merge branch 'laptop'
2011-07-23 01:44:54 -04:00
e23cb27451
Modified MD5 to account for the triple hets that shouldn't be phased
2011-07-23 01:44:44 -04:00
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
Eric Banks
Mauricio Carneiro
Kiran V Garimella
Mark DePristo
Matt Hanna