3226d5dc0d
Merge branch 'master' into ped
2011-10-05 15:03:09 -07:00
e7c80f7c45
Renaming quantitative trait to OtherPhenotype which is now a String not a double
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-- 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
51ecc20867
getFamily() and associated methods implemented and tested
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-- Sample no longer serializable
-- Sample now implements Comparable
2011-10-05 09:55:05 -07:00
f4bac58f14
Merged bug fix from Stable into Unstable
2011-10-04 21:00:34 -07:00
d1d39943d0
Updating MD5 for BAMs that I added a read group to, part 2
2011-10-04 21:00:15 -07:00
9bd3ba4c7e
Missed one MD5
2011-10-04 16:04:52 -07:00
ffdfdcde3f
Updating MD5s
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-- Interval test now uses RG containing BAM
-- DoC sample name ordering has changed.
2011-10-04 15:54:45 -07:00
463eab7604
All MD5 mismatches for test are shown
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-- 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
c642a080d4
Merged bug fix from Stable into Unstable
2011-10-04 14:08:41 -07:00
941317167e
Updating MD5 for BAMs that I added a read group to
2011-10-04 14:08:00 -07:00
e1d6c7a50a
Updating MD5 that have changed due to sample ordering differences
2011-10-04 09:33:23 -07:00
343a7b6b2f
Updating UG integration tests for arbitrary impact of sample order changes on downsampling
2011-10-04 08:14:00 -07:00
a27641e1fc
Cleaned up imports
2011-10-04 06:28:36 -07:00
b20689ff55
No longer supports extraProperties
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-- 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
867a7476c1
Systematic unit tests for the sample object
2011-10-03 19:09:02 -07:00
3837aa45b4
Fixing conflicts
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Conflicts:
public/java/test/org/broadinstitute/sting/utils/clipreads/ReadClipperUnitTest.java
2011-10-03 19:07:59 -07:00
2e3dc52088
Minor function renaming
2011-10-03 14:41:13 -07:00
dd71884b0c
On path to SampleDB engine integration
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-- PedReader tag parser
-- Separation of SampleDBBuilder from SampleDB (now immutable)
-- Removed old sample engine arguments
2011-10-03 12:08:07 -07:00
89ac50e86e
SampleDataSource -> SampleDB
2011-10-03 09:33:30 -07:00
93fba06cb5
Support for whitespace only lines
2011-10-03 09:30:10 -07:00
0604ce55d1
PedReader support for ; separated lines, not only newline
2011-10-03 09:19:58 -07:00
52f670c8b8
100% version of PedReader
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-- Passes all unit tests
-- Added unit tests for missing fields
2011-10-03 06:12:58 -07:00
bf6a3a6532
Added framework to do batch CigarClip Testing
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*NOTE: This commit has not been compiled!
2011-10-02 22:33:46 -04:00
dd75ad9f49
95% PedReader
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-- 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
84160bd83f
Reorganization of Sample
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-- 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
56f10b40a8
Fixing test bugs for WindowMaker that required empty sample list
2011-09-30 14:18:27 -04:00
30d23942b1
Renamed ReadBackedPileup getXSampleName() functions to getXSample
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-- now that we don't have Sample objects floating around we don't have to have all of the Name extensions on our functions
2011-09-30 10:02:57 -04:00
e055a78f6e
LIBS now requires at least one sample be present
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-- UnitTest provides a "null" sample for matching the reads without read groups
2011-09-30 09:49:35 -04:00
b71b51751e
Bug fix for UnitTest
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-- Provide the null sample to the LIBS, as this seems to be required for correctly passing this unit test
-- Will be fixed in a future update
2011-09-29 17:30:01 -04:00
1765fbeb6b
Merge branch 'master' into ped
2011-09-29 17:18:51 -04:00
98ecaf8aa0
Support for ReducedReads with reduced counts and average quals
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-- ReadUtils and UnitTest updated to support new byte[] style
-- Removed unnecessary read transformer in PairHMM
2011-09-29 17:18:39 -04:00
9458f01409
Test cleanup of Sample object
2011-09-29 15:13:05 -04:00
625ffb6a07
LocusIteratorByState and ReadBackedPileups no long use Sample
2011-09-29 14:52:11 -04:00
505416b6c0
Merge branch 'master' into ped
2011-09-29 12:22:39 -04:00
4086fa768f
Disabling all ReadClipperUnitTests
2011-09-29 12:20:35 -04:00
5043d76c3d
Removing more bad uses of SampleDataSource creation
2011-09-29 12:16:34 -04:00
5c9227cf5e
Further cleanup of Sample database
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-- Removing more and more unnecessary code
-- Partial removal of type safe Sample usage. On the road to SampleDB only
2011-09-29 11:50:05 -04:00
2a0cd556d3
Further cleanup of Sample
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-- Cleaned up interface functions in GAE
-- Added Walker.getSampleDB() function which is an easier option for tools to get the samples db
2011-09-29 10:34:51 -04:00
e76f381628
Moved sample package from DataSources to gatk, and renamed it samples
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-- All associated changes to the codebase are just header updates
2011-09-29 09:57:15 -04:00
fc86cd6fd8
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/carneiro/gatk/RR into rr
2011-09-29 00:12:15 -04:00
4fd5630f6a
Added ReadClipper Unit Test
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* Includes tests that include HardClip to Read and Reference Coords.
* Changed ReadUtils.HardClipByReferenceCoordinates from private to protected to allow for testing
2011-09-28 23:13:50 -04:00
9272ed03b5
Merged bug fix from Stable into Unstable
2011-09-28 21:26:43 -04:00
0acaf2df65
Fix an embarrassing issue where a specific configuration of minimal coverage
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over small intervals could cause reads to be dropped from the pileup. Nothing
to see here...
2011-09-28 21:23:01 -04:00
4f09453470
Refactored reduced read utilities
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-- UnitTests for key functions on reduced reads
-- PileupElement calls static functions in ReadUtils
-- Simple routine that takes a reduced read and fills in its quals with its reduced qual
2011-09-26 12:58:31 -04:00
3eef800889
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-24 21:20:11 -04:00
4707ab4a7d
Added unit tests to test genotype merges with PL's
2011-09-24 21:17:15 -04:00
203517fbb7
a) Cleanups/bug fixes to previous commit to CombineVariants.
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b) Change md5 to reflect records that are now merged correctly.
c) Change unit merge alleles test to reflect the fact that a null non-variant vc object is not valid and not supported because there's no way to codify such object in a vcf. The code correctly converts this to a non-variant single-base event with whatever the reference is at that location.
2011-09-24 19:08:00 -04:00
cd058dd10f
a) Fixed md5 for legit change in UG output that now also no-calls genotypes w/0,0,0 in PL's in SNP case.
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b) First reimplementation of new vc merger of different types. Previous version did it in two steps, first merging all vc's per type and then trying to see if resulting vc's would be merged if alleles of one type were a subset of another, but this won't work when uniquifying genotypes since sample names would be messed up and GT sample names wouldn't match VC sample names. Now, it's actually simpler: when splitting vc's by type before merging, we check for alleles of one vc being a subset of alleles of vc of another type and if so we put them together in same list.
2011-09-24 13:40:11 -04:00
8d9e136bba
Merge branch 'stable'
2011-09-24 09:26:28 -04:00
f792353dcd
Framework for genotype unit test
2011-09-24 08:56:45 -04:00
Mark DePristo
Mauricio Carneiro
Roger Zurawicki
Matt Hanna
Guillermo del Angel