d0ab6bf7a9
Now links to sub and superclass documentation, where possible.
2011-07-24 09:56:17 -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
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
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
28b9432d26
Docs for read filters, the engine, and the UserExceptions.
2011-07-22 16:09:21 -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
9e88d51db9
Removed now unused @version tags from walker docs.
2011-07-22 09:57:03 -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
e922ebc29d
Missed this template for walker index.
2011-07-22 09:13:33 -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
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
664246937c
Try to resolve merge conflict
2011-07-21 10:19:26 -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
4b0b7f4b32
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-20 14:49:25 -04:00
f14f20d718
Fix bug involving reuse of the sample variable.
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Cleaned up some otherwise unused comments and code.
2011-07-20 14:48:33 -04:00
0a1d2df8cb
Merged bug fix from Stable into Unstable
2011-07-20 13:19:35 -04:00
f15023b7d2
Bad bug fix: output GLs in multiallelic records were in incorred order (misread spec)
2011-07-20 12:10:48 -04:00
c09f92ccee
Fixing the illegal character accidently entered
2011-07-20 11:39:04 -04:00
4e00666632
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-20 11:38:16 -04:00
ea90af199c
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-20 11:17:36 -04:00
d3a8363491
Changed MRAV to ADAV
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Updated ReducedBAMEvaluation to allow multiple parameters to be tested
Fixed previous error
2011-07-20 10:49:50 -04:00
b9c9e0e952
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-20 10:45:16 -04:00
7140280bf6
Further bug fixes/cleanups for PrintReadsWalker
2011-07-20 10:44:37 -04:00
a2d90a3590
Bug fix: reverted logic so that default behavior skips over sample lookup
2011-07-20 10:23:10 -04:00
e8409c80fa
Further protection vs null pointers in PrintReadsWalker
2011-07-19 21:59:24 -04:00
5d706c9e92
Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
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Removing PSP and CSM
Conflicts:
public/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/CreateSequenomMask.java
public/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java
2011-07-19 20:25:33 -04:00
fb2d475c22
Bug fix to prevent null pointer
2011-07-19 20:13:56 -04:00
92c7cfa1c8
BWA bindings and tests moved to public (was required for ValidationAmplicons)
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Integration tests for ValidationAmplicons. New argument to disable BWA, lowercase letters only for repetitiveness instead.
2011-07-19 20:11:31 -04:00
baae381acb
Revert "Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable"
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This reverts commit 039a6bb01f345322ce2be50ae3634308bb24e77e, reversing
changes made to b9c9973d1c638dfc9f8c19b5eb845e99844f9d29.
2011-07-19 18:38:53 -04:00
Mark DePristo
Khalid Shakir
Mauricio Carneiro
Eric Banks
Matt Hanna
Guillermo del Angel
Christopher Hartl
Roger Zurawicki
David Roazen