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
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
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
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
eb63b48414
Revert "Resolving conflict"
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This reverts commit 87f0d4a8b0627b3be86acdfef5a9f2fc6ea923ee.
2011-07-19 18:36:53 -04:00
a3cecf0668
Resolving conflict
2011-07-19 17:20:27 -04:00
3d72b98a35
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
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Conflicts:
private/java/test/org/broadinstitute/sting/gatk/walkers/reducereads/ReduceReadsIntegrationTest.java
2011-07-19 17:16:20 -04:00
d92d00a85d
Changed MRAV to ADAV to reflect real implementation (Max reads to Average Depth at Variant Sites).
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Optimized Mapping Quality calculation.
Correctly filtered reads below minimum Mapping Quality threshold
2011-07-19 16:59:06 -04:00
8a7e698883
better debug output for plotting.
2011-07-19 15:28:54 -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
6181d1e4cb
Fixed integration test for VariantsToTable: now the * in REF column is not output
2011-07-19 14:42:11 -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
005adf377f
Derive MEDIAN_INSERT_SIZE plot from base plot with additional faceting.
2011-07-19 10:48:45 -04:00
9a1394d7e7
Clean up MEDIAN_INSERT_SIZE plot for consistency with other plots.
2011-07-19 10:34:50 -04:00
5d3112c665
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-19 09:32:01 -04:00
0cec2c6759
When sorting samples by date, only use filtered samples to avoid discontinuities
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in the plot. Add brief documentation for running the R script.
2011-07-19 09:28:51 -04:00
9ad5c7dfa4
Resolving simple conflicts in the data processing pipeline.
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Conflicts:
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
2011-07-19 08:05:11 -04:00
7688bda1a6
better progress report for the DPP
2011-07-18 23:39:47 -04:00
2b465ab43b
* added optional 'no validation' for the Data Processing pipeline.
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* some simplifications on the picard classes
2011-07-18 23:30:31 -04:00
4cf7a2af23
Removed broad specific default paths so people from outside the broad can use it.
2011-07-18 23:25:21 -04:00
9b446020f9
Using picard implementations for accessing aggregation directories.
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Added more utilities to PicardPrivate.
Revved picard.
2011-07-18 21:49:03 -04:00
0ef37979cc
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-18 21:30:51 -04:00
d5d107856c
Subselect based on bait set.
2011-07-18 18:42:21 -04:00
1837da37f6
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-18 17:59:26 -04:00
916c0c9489
some quick & dirty debug info for the replication validation walker.
2011-07-18 17:57:12 -04:00
044f5faa4d
Support for numeric columns.
2011-07-18 17:44:49 -04:00
9729d61e2d
Use geom_text() instead of geom_point() when outputting data for new project
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only.
2011-07-18 17:29:00 -04:00
f1e3c3356b
Merge branch 'rbam'
2011-07-18 17:26:07 -04:00
c618a5b54c
commented out wrong MD5s
2011-07-18 17:25:45 -04:00
a9f956c80c
Fixed several bugs in the pooled caller. Creating a good dataset to test its accuracy now.
2011-07-18 16:04:11 -04:00
4e78f0b064
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-18 15:45:23 -04:00
8f0badc52b
Updating md5s, as the diffobjects walker now emits the summary in reverse order.
2011-07-18 15:44:21 -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
Mauricio Carneiro
Roger Zurawicki
Guillermo del Angel
Christopher Hartl
David Roazen
Matt Hanna
Khalid Shakir