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6497 Commits (6fa17d86ae8fecc4a0bd1c9e54f82ee0c8866d3f)

Author SHA1 Message Date
Mark DePristo 6fa17d86ae Completely hacked together version of a FreeMarker + javadoc + custom doclet walker documentation generator 2011-07-21 00:18:07 -04:00
Mark DePristo 45c73ff0e5 Runs and emits an HTML document 2011-07-20 17:16:33 -04:00
Mauricio Carneiro c09f92ccee Fixing the illegal character accidently entered 2011-07-20 11:39:04 -04:00
Mauricio Carneiro 4e00666632 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-20 11:38:16 -04:00
Roger Zurawicki ea90af199c Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-20 11:17:36 -04:00
Roger Zurawicki d3a8363491 Changed MRAV to ADAV 
Updated ReducedBAMEvaluation to allow multiple parameters to be tested
Fixed previous error
 2011-07-20 10:49:50 -04:00
Guillermo del Angel b9c9e0e952 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-20 10:45:16 -04:00
Guillermo del Angel 7140280bf6 Further bug fixes/cleanups for PrintReadsWalker 2011-07-20 10:44:37 -04:00
Guillermo del Angel a2d90a3590 Bug fix: reverted logic so that default behavior skips over sample lookup 2011-07-20 10:23:10 -04:00
Guillermo del Angel e8409c80fa Further protection vs null pointers in PrintReadsWalker 2011-07-19 21:59:24 -04:00
Christopher Hartl 5d706c9e92 Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 
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
Guillermo del Angel fb2d475c22 Bug fix to prevent null pointer 2011-07-19 20:13:56 -04:00
Christopher Hartl 92c7cfa1c8 BWA bindings and tests moved to public (was required for ValidationAmplicons) 
Integration tests for ValidationAmplicons. New argument to disable BWA, lowercase letters only for repetitiveness instead.
 2011-07-19 20:11:31 -04:00
David Roazen baae381acb Revert "Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable" 
This reverts commit 039a6bb01f345322ce2be50ae3634308bb24e77e, reversing
changes made to b9c9973d1c638dfc9f8c19b5eb845e99844f9d29.
 2011-07-19 18:38:53 -04:00
David Roazen eb63b48414 Revert "Resolving conflict" 
This reverts commit 87f0d4a8b0627b3be86acdfef5a9f2fc6ea923ee.
 2011-07-19 18:36:53 -04:00
Roger Zurawicki a3cecf0668 Resolving conflict 2011-07-19 17:20:27 -04:00
Roger Zurawicki 3d72b98a35 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable 
Conflicts:
	private/java/test/org/broadinstitute/sting/gatk/walkers/reducereads/ReduceReadsIntegrationTest.java
 2011-07-19 17:16:20 -04:00
Roger Zurawicki d92d00a85d Changed MRAV to ADAV to reflect real implementation (Max reads to Average Depth at Variant Sites). 
Optimized Mapping Quality calculation.
 Correctly filtered reads below minimum Mapping Quality threshold
 2011-07-19 16:59:06 -04:00
Mauricio Carneiro 8a7e698883 better debug output for plotting. 2011-07-19 15:28:54 -04:00
Christopher Hartl 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
Guillermo del Angel 6181d1e4cb Fixed integration test for VariantsToTable: now the * in REF column is not output 2011-07-19 14:42:11 -04:00
Guillermo del Angel e6d306458c Merge bug fixes 2011-07-19 14:36:20 -04:00
Guillermo del Angel 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
Matt Hanna 005adf377f Derive MEDIAN_INSERT_SIZE plot from base plot with additional faceting. 2011-07-19 10:48:45 -04:00
Matt Hanna 9a1394d7e7 Clean up MEDIAN_INSERT_SIZE plot for consistency with other plots. 2011-07-19 10:34:50 -04:00
Matt Hanna 5d3112c665 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-19 09:32:01 -04:00
Matt Hanna 0cec2c6759 When sorting samples by date, only use filtered samples to avoid discontinuities 
in the plot.  Add brief documentation for running the R script.
 2011-07-19 09:28:51 -04:00
Mauricio Carneiro 9ad5c7dfa4 Resolving simple conflicts in the data processing pipeline. 
Conflicts:
	public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
 2011-07-19 08:05:11 -04:00
Mauricio Carneiro 7688bda1a6 better progress report for the DPP 2011-07-18 23:39:47 -04:00
Mauricio Carneiro 2b465ab43b * added optional 'no validation' for the Data Processing pipeline. 
* some simplifications on the picard classes
 2011-07-18 23:30:31 -04:00
Mauricio Carneiro 4cf7a2af23 Removed broad specific default paths so people from outside the broad can use it. 2011-07-18 23:25:21 -04:00
Khalid Shakir 9b446020f9 Using picard implementations for accessing aggregation directories. 
Added more utilities to PicardPrivate.
Revved picard.
 2011-07-18 21:49:03 -04:00
Matt Hanna 0ef37979cc Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-18 21:30:51 -04:00
Matt Hanna d5d107856c Subselect based on bait set. 2011-07-18 18:42:21 -04:00
Mauricio Carneiro 1837da37f6 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-18 17:59:26 -04:00
Mauricio Carneiro 916c0c9489 some quick & dirty debug info for the replication validation walker. 2011-07-18 17:57:12 -04:00
Matt Hanna 044f5faa4d Support for numeric columns. 2011-07-18 17:44:49 -04:00
Matt Hanna 9729d61e2d Use geom_text() instead of geom_point() when outputting data for new project 
only.
 2011-07-18 17:29:00 -04:00
Mauricio Carneiro f1e3c3356b Merge branch 'rbam' 2011-07-18 17:26:07 -04:00
Mauricio Carneiro c618a5b54c commented out wrong MD5s 2011-07-18 17:25:45 -04:00
Mauricio Carneiro 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
Mark DePristo 4e78f0b064 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-18 15:45:23 -04:00
Mark DePristo 8f0badc52b Updating md5s, as the diffobjects walker now emits the summary in reverse order. 2011-07-18 15:44:21 -04:00
Mark DePristo 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 782a05e9b5 Support for sorting the diff output in reverse order. 2011-07-18 15:43:01 -04:00
Mark DePristo 45702d3084 Now supports a mode where the primary key isn't sorted. In this case the records are displayed in the order in which they are added to to the table. 2011-07-18 15:40:15 -04:00
Matt Hanna 15b44ac2c3 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-18 14:56:41 -04:00
Matt Hanna e5e7523f8b Modify to support either bam list format files or tsv formatted files. The 
latter provide a major advantage when dealing with samples with spaces in the
names.
 2011-07-18 14:56:00 -04:00
Matt Hanna adce37774a Add functionality for tsv output. 2011-07-18 14:12:01 -04:00
Eric Banks 6d5e87da10 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-18 13:59:10 -04:00