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
...
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
6fd6684e86
Merged bug fix from Stable into Unstable
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Conflicts:
build.xml
2011-07-25 15:21:17 -04:00
6f43284053
Switch to including our entire exception tree rather than just UserException.
2011-07-25 15:19:41 -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
af0b5883c3
In unstable, add a reference to DocumentedGATKFeature to vcf.jar, which is now
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a static dependency of UserExceptions.
2011-07-25 14:36:12 -04:00
6c49197de6
Merged bug fix from Stable into Unstable
2011-07-25 14:32:33 -04:00
a00e302321
Fix formatting issue.
2011-07-25 14:31:40 -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
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
5db05d2873
Refactored Mills codecs so that they're in correct packages
2011-07-25 10:25:25 -04:00
115879b31f
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-25 10:13:16 -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
e602166f78
First fully functional version outputting a full vcf
2011-07-24 19:38:59 -04:00
7b84347047
Main index is sorted by the template now.
2011-07-24 18:19:40 -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
b8db0510e0
Sytle sheet and common functions
2011-07-24 15:43:23 -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
e0cb403b33
A read walker for contig statistics
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I used this walker for my mtdna analysis where the goal was to see how the chromosomes were represented by the sequences in the bam files. It is very useful as a first look at a new dataset if you want to have an idea of where most of the reads fall. It reports the number of reads in each contig, percetages, enrichment as well as the expected number of reads for each contig and enrichment given the size of your dataset. I will document it accordingly with the new documentation tool. It's in public, and I'm happy to support it.
2011-07-24 02:36:17 -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
ac3eaf5d54
Next intermediate version of MillsGenotypeDecoderWalker
2011-07-23 17:30:37 -04:00
1f8fc4a041
Added edu.mit.broad.picard to Queue packaged jar.
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Added hack to workaround EDU.oswego namespace and staging on mac case-insensitive filesystems.
2011-07-23 14:40:29 -04:00
dcf21f379a
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-07-23 12:59:53 -04:00
f0a6dd27a1
Renaming the plot output directory names.
2011-07-23 12:59:37 -04:00
0b36b6540f
Merge branch 'laptop'
2011-07-23 01:44:54 -04:00
Mark DePristo
Matt Hanna
Kiran V Garimella
Guillermo del Angel
Mauricio Carneiro
Khalid Shakir