38969b9783
Prototype of RODBinding @Arguments instead of -B syntax
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Initial version of RodBinding class.
Flow from walker Rodbinding @Arguments -> RMDTriplet (old system) -> GATK engine (standard). Will need refactoring.
2011-07-26 11:09:06 -04:00
f3049fba63
refdata directory cleanup
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Removing unused files RODRecordIterator, ReferenceOrderedData, QueryableTrack, RMDTrackCreationException, GATKFeatureIterator, ReferenceOrderedDataUnitTest
Refactored dbSNP and refseq utilities to be closer to the other files implementing these features
2011-07-25 13:21:52 -04:00
90947ab359
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-25 12:53:56 -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
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
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
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
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
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
5af9d50183
Merge branch 'laptop'
2011-07-23 01:12:06 -04:00
5521919cc9
Fixed bug where variants to phase were not being selected properly.
2011-07-23 01:11:28 -04:00
7da99388ac
Merge branch 'laptop'
2011-07-23 01:01:11 -04:00
58eed20b83
Copy all entries from the attributes map, rather than attempting to modify an unmodifiable map.
2011-07-23 01:00:46 -04:00
ffa361f57f
Merge branch 'laptop'
2011-07-23 00:50:38 -04:00
9417ba8c2c
Modified to accept multi-sample VCFs, removed the application of filters, and changed transmission probability field to be a genotype field rather than an INFO field.
2011-07-23 00:48:26 -04:00
051c1dc639
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-22 15:59:00 -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
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
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
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
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
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
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
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
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
07e716d23a
PickSequenomProbes2 expanded functionality: lowercasing based on sequence uniqueness, preserving reference base prior to indel (not a part of the VC as I thought it was), masking deletion bases with 'N's, flanking insertion with 'N's, output is a fasta formatted file. Renamed to ValidationAmplicons since this is really not for picking sequenom probes, but for generating amplicon sequence from which other applications (like sequenom) can choose PCR primers. Moved from private to public.
2011-07-19 15:21:47 -04:00
e6d306458c
Merge bug fixes
2011-07-19 14:36:20 -04:00
989dd17f95
a) Add ability in PrintReads to specify a sample file to easily subset samples, useful for IGV visualization, b) VariantsToTable is more R-friendly with Indels when printing ref/alt columns, c) Changes to SelectVariants ability to speficy a mask to randomly sample from a given AF distribution
2011-07-19 14:29:07 -04:00
c05451047c
Support for multiple records at the same site. The first record gets chr:start, and subsequent records get chr:start_2, chr:start_3, etc.
2011-07-18 15:43:52 -04:00
Mark DePristo
Kiran V Garimella
Christopher Hartl
Matt Hanna
Guillermo del Angel
David Roazen