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Author SHA1 Message Date
Mark DePristo b068846407 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-10-05 17:12:09 -07:00
Khalid Shakir 6d6149b9a2 Updated gsalib gsa.read.gatkreport to return all reports, even those beginning with '.'. 
In PreQC using geom_blank() so MEDIAN_INSERT_SIZE plot doesn't crash on facet_grid(scales='free') when data doesn't contain points for 'RF' or 'TANDEM'.
 2011-10-05 18:30:40 -04:00
Matt Hanna 982983355f Merged bug fix from Stable into Unstable 2011-10-05 18:27:29 -04:00
Matt Hanna dd780dba5f Rather than just picking a few classes to be the roots of the vcf jar and 
including all dependencies, use the entire codecs.vcf and variantcontext
packages as roots.

Fix for my fix for Jim Robinson.
 2011-10-05 18:25:26 -04:00
Mark DePristo a91509e7dd Shouldn't be public 2011-10-05 15:22:57 -07:00
Mark DePristo be2d29ce69 Final PED documentation 2011-10-05 15:17:41 -07:00
Mark DePristo 3226d5dc0d Merge branch 'master' into ped 2011-10-05 15:03:09 -07:00
Mark DePristo 6a573437af Details documentation arguments for -ped 2011-10-05 15:00:58 -07:00
David Roazen dc6d71dec5 Merged bug fix from Stable into Unstable 2011-10-05 16:53:32 -04:00
David Roazen b732f740d2 Revert "Change vcf jar to use a classfileset to pull all dependencies. Should save" 
This reverts commit 441022c4c600624928da46419a6a289200700f3e.
 2011-10-05 16:51:30 -04:00
Mark DePristo e7c80f7c45 Renaming quantitative trait to OtherPhenotype which is now a String not a double 
-- we can now use PED file to represent population data or other arbitrary phenotype data, not just doubles
 2011-10-05 12:26:33 -07:00
Mark DePristo 51ecc20867 getFamily() and associated methods implemented and tested 
-- Sample no longer serializable
-- Sample now implements Comparable
 2011-10-05 09:55:05 -07:00
Mark DePristo f4bac58f14 Merged bug fix from Stable into Unstable 2011-10-04 21:00:34 -07:00
Mark DePristo d1d39943d0 Updating MD5 for BAMs that I added a read group to, part 2 2011-10-04 21:00:15 -07:00
Mark DePristo 9bd3ba4c7e Missed one MD5 2011-10-04 16:04:52 -07:00
Mark DePristo ffdfdcde3f Updating MD5s 
-- Interval test now uses RG containing BAM
-- DoC sample name ordering has changed.
 2011-10-04 15:54:45 -07:00
Mark DePristo a45d985818 TODO method stubs 2011-10-04 15:54:09 -07:00
Mark DePristo 463eab7604 All MD5 mismatches for test are shown 
-- Now for tests like DoC, with 20 output md5s, you see all of the differences before failing.
 2011-10-04 15:53:52 -07:00
Mark DePristo c642a080d4 Merged bug fix from Stable into Unstable 2011-10-04 14:08:41 -07:00
Mark DePristo 941317167e Updating MD5 for BAMs that I added a read group to 2011-10-04 14:08:00 -07:00
Matt Hanna 4ebdc52b0d Merged bug fix from Stable into Unstable 2011-10-04 13:16:20 -04:00
Matt Hanna 88c2fad64f Change vcf jar to use a classfileset to pull all dependencies. Should save 
Jim Robinson some detective work in the long run.
 2011-10-04 13:14:39 -04:00
Mark DePristo e1d6c7a50a Updating MD5 that have changed due to sample ordering differences 2011-10-04 09:33:23 -07:00
Mark DePristo 343a7b6b2f Updating UG integration tests for arbitrary impact of sample order changes on downsampling 2011-10-04 08:14:00 -07:00
Mark DePristo fee89e47ff Only throws an error when there are no samples but there are reads 
-- Handles the case when you are running a ROD traversal and yet the LIBS is still used to return null everywhere.
 2011-10-04 06:50:54 -07:00
Mark DePristo f552aede42 Only provide the sample names in the BAM file for efficiency 2011-10-04 06:50:12 -07:00
Mark DePristo a27641e1fc Cleaned up imports 2011-10-04 06:28:36 -07:00
Mauricio Carneiro 8b4a27092d Merge branch 'master' into rr 2011-10-03 19:46:04 -07:00
Mauricio Carneiro 6ca162ae9a Not pre-sorted. 
Turns out it is a complicated solution when going multi-sample, so I'll leave it off for now.
 2011-10-03 19:45:46 -07:00
Mark DePristo b20689ff55 No longer supports extraProperties 
-- the underlying data structure is still present, but until I decide what to do for the extensible system I've completely disabled the subsystem
-- Added code to merge Samples, so that a mostly full record can be merged with a consistent empty record.  If the two records are inconsistent, an error is thrown
-- addSample() in Sample.class now invokes mergeSample() when appropriate
-- Validation types are now only STRICT or SILENT
-- Validation code implemented in SampleDBBuilder
-- Extensive unit tests for SampleDBBuilder
 2011-10-03 19:20:33 -07:00
Mark DePristo 867a7476c1 Systematic unit tests for the sample object 2011-10-03 19:09:02 -07:00
Mauricio Carneiro 3837aa45b4 Fixing conflicts 
Conflicts:
	public/java/test/org/broadinstitute/sting/utils/clipreads/ReadClipperUnitTest.java
 2011-10-03 19:07:59 -07:00
Mark DePristo 2e3dc52088 Minor function renaming 2011-10-03 14:41:13 -07:00
Mark DePristo dd71884b0c On path to SampleDB engine integration 
-- PedReader tag parser
-- Separation of SampleDBBuilder from SampleDB (now immutable)
-- Removed old sample engine arguments
 2011-10-03 12:08:07 -07:00
Eric Banks c3eff7451a Found a small inefficiency while profiling: we were still using String.split instead of ParsingUtils.split to break up array values in the INFO field. There was a noticeable (albeit not big) difference in the change when reading sites only files. 2011-10-03 14:20:39 -04:00
Mark DePristo 8ee0f91904 Remove residual processing tracker arguments 2011-10-03 09:50:01 -07:00
Mark DePristo 89ac50e86e SampleDataSource -> SampleDB 2011-10-03 09:33:30 -07:00
Mark DePristo 93fba06cb5 Support for whitespace only lines 2011-10-03 09:30:10 -07:00
Mark DePristo 0604ce55d1 PedReader support for ; separated lines, not only newline 2011-10-03 09:19:58 -07:00
Mark DePristo 52f670c8b8 100% version of PedReader 
-- Passes all unit tests
-- Added unit tests for missing fields
 2011-10-03 06:12:58 -07:00
Roger Zurawicki bf6a3a6532 Added framework to do batch CigarClip Testing 
*NOTE: This commit has not been compiled!
 2011-10-02 22:33:46 -04:00
Mark DePristo dd75ad9f49 95% PedReader 
-- Passes significiant unit tests
-- Implicit sample creation for mom / dad when you create single samples
-- Continuing cleanup of Sample and SampleDataSource
 2011-09-30 18:03:34 -04:00
Andrey Sivachenko c7898a9be7 inconsequential change in string constants printed into the vcf which noone uses anyway... 2011-09-30 16:40:21 -04:00
Mark DePristo 010899f886 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-09-30 15:51:09 -04:00
Mark DePristo 84160bd83f Reorganization of Sample 
-- Moved Gender and Afflication to separate public enums
-- PedReader 90% implemented
-- Improve interface cleanup to XReadLines and UserException
 2011-09-30 15:50:54 -04:00
Mauricio Carneiro 05fba6f23a Clipping ends inside deletion and before insertion 
fixed.
 2011-09-30 15:44:43 -04:00
Mauricio Carneiro e0b771c233 Pre-sorting output 
sorting variable regions independently to make the output pre-sorted. Major speedup.
 2011-09-30 15:44:43 -04:00
Mauricio Carneiro b5bdea1cb9 Fix: hardclip first interval overlap but overlap subsequent intervals 
If a read had the left tail clipped (that would overlap the current interval) but the right tail overlaps other intervals, this was triggering out of order reads to get processed before they should. Fixed.
 2011-09-30 15:44:43 -04:00
Mauricio Carneiro d211b3b7f0 Fixing interval overlap logic 
Complete re-write of the optimized interval overlap logic. Added lots of exceptions to trap  future wrongdoings.
 2011-09-30 15:44:42 -04:00
Mark DePristo c1cf6bc45a PEDReader should be in samples 2011-09-30 14:22:19 -04:00