1865211b6d
Merged bug fix from Stable into Unstable
2011-07-27 22:52:06 -04:00
6230315ff2
Along with my half-written commit message from earlier, I also forgot to commit the integration test updates. This is what happens when you try to do things 30 seconds before you leave for the day. To finish up from before: complex events weren't being padded with the reference base as per the VCF spec. They are now.
2011-07-27 22:51:21 -04:00
f3ad4ec94b
Removed annoying FastaSequenceIndexBuilderProgressListener infrastructure that was just a boolean switch on whether to print progress or not.
2011-07-27 22:06:23 -04:00
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
15be383d5b
Merge branch 'master' into rodRefactor
2011-07-27 15:36:49 -04:00
38a2518668
Merge branch 'master' into rodRefactor
2011-07-27 15:34:54 -04:00
60db6cc836
Warnings for old ROD system use.
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Removed unused class GATKRODFeature
2011-07-27 12:39:12 -04:00
097828a466
ParsingEngine now maintains the list of rodBindings
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No longer try to reparser objects to find the right fields
Direct support in RodBinding for getTags()
2011-07-27 11:36:53 -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
9dfb57168a
RodBinding source is no longer assumed to be a file
2011-07-26 13:59:44 -04:00
d0badd5bd6
RodBinding subclassed to VariantContextRodBinding for easy access to VariantContext providing RODs
2011-07-26 13:54:55 -04:00
7ab8b53339
Support for List<RodBinding> argument type
2011-07-26 11:37:31 -04:00
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
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
2a51543693
Actually should have been gone...
2011-07-25 13:27:42 -04:00
ebfd8df06c
Restoring accidentially deleted unit test
2011-07-25 13:25:30 -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
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
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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
f366124778
Merge branch 'laptop'
2011-07-23 01:25:36 -04:00
45f2ca8d99
Changed MD5 to reflect latest changes to PhaseByTransmission.
2011-07-23 01:21:07 -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
b5deff48e6
Merge branch 'laptop'
2011-07-23 00:56:50 -04:00
5638017137
Removed the nofilters argument specification in the integrationtest
2011-07-23 00:56:23 -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
28b9432d26
Docs for read filters, the engine, and the UserExceptions.
2011-07-22 16:09:21 -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
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
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
172b35372b
Moved all of the distributed GATK code to archive.
2011-07-22 09:20:32 -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
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
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
6fa17d86ae
Completely hacked together version of a FreeMarker + javadoc + custom doclet walker documentation generator
2011-07-21 00:18:07 -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
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
Eric Banks
Mark DePristo
Mauricio Carneiro
Kiran V Garimella
Matt Hanna
Khalid Shakir
Christopher Hartl
Guillermo del Angel