4ebdc52b0d
Merged bug fix from Stable into Unstable
2011-10-04 13:16:20 -04:00
88c2fad64f
Change vcf jar to use a classfileset to pull all dependencies. Should save
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Jim Robinson some detective work in the long run.
2011-10-04 13:14:39 -04:00
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
fee89e47ff
Only throws an error when there are no samples but there are reads
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-- 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
f552aede42
Only provide the sample names in the BAM file for efficiency
2011-10-04 06:50:12 -07:00
a27641e1fc
Cleaned up imports
2011-10-04 06:28:36 -07:00
8b4a27092d
Merge branch 'master' into rr
2011-10-03 19:46:04 -07:00
6ca162ae9a
Not pre-sorted.
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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
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
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
8ee0f91904
Remove residual processing tracker arguments
2011-10-03 09:50:01 -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
c7898a9be7
inconsequential change in string constants printed into the vcf which noone uses anyway...
2011-09-30 16:40:21 -04:00
010899f886
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-30 15:51:09 -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
05fba6f23a
Clipping ends inside deletion and before insertion
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fixed.
2011-09-30 15:44:43 -04:00
e0b771c233
Pre-sorting output
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sorting variable regions independently to make the output pre-sorted. Major speedup.
2011-09-30 15:44:43 -04:00
b5bdea1cb9
Fix: hardclip first interval overlap but overlap subsequent intervals
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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
d211b3b7f0
Fixing interval overlap logic
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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
c1cf6bc45a
PEDReader should be in samples
2011-09-30 14:22:19 -04:00
56f10b40a8
Fixing test bugs for WindowMaker that required empty sample list
2011-09-30 14:18:27 -04:00
73577b72cf
Misc minor updates in HaplotypeCaller
2011-09-30 13:41:24 -04:00
af6c053435
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-30 13:33:31 -04:00
810e8ad011
Removed getXByReaders() function from the engine
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-- These could be simplied in their downstream uses
-- Or they could be replaced with a generic getSAMFileHeaders() function and then apply the getSamples(header) as desired downstream
2011-09-30 10:43:51 -04:00
f75573dd54
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-30 10:35:26 -04:00
6637cd9dd5
Fixes to CalibrateGenotypeLikelihoods: a) Fix up the walker itself which was broken since the new rod binding system, b) added ability to do indels and to optionally test banded implementation, c) experimental ability to do multiple samples (may need more work)
2011-09-30 10:35:10 -04:00
178ba24c27
Move getSamplesForSamFile to SampleUtils
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-- A nearly identical piece of code already lived in SampleUtils. Now there are two functions, one taking a regular header and another grabbing the merged header from the GATK engine itself. Much cleaner
2011-09-30 10:28:18 -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
3289a325fc
Removed final use of Sample in RBP
2011-09-30 09:57:39 -04:00
a69a4dda2f
SamplesDB no longer has null sample
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-- Updated getSamples().size() == 2 test in CallableLociWalker that really ensured there was one sample in the system
2011-09-30 09:56:23 -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
9860a2c989
Merge branch 'master' into ped
2011-09-30 09:28:18 -04:00
a881d6f145
Now only generates the poly VCF with select variants if the file doesn't exist
2011-09-30 08:42:09 -04:00
d901fed617
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-30 08:41:44 -04:00
cabacf028d
Intermediate commit to fix interval skipping
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may need additional testing.
2011-09-29 18:45:12 -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
9508220157
fixed hard clipping both ends inside deletion
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If both ends of the interval falls within a deletion in the read then hardClipBothEnds would cut the right tail first including the entire deletion, then fail to cut the left tail because there would not be any bases there anymore. Fixed.
2011-09-29 15:36:49 -04:00
9458f01409
Test cleanup of Sample object
2011-09-29 15:13:05 -04:00
Matt Hanna
Mark DePristo
Mauricio Carneiro
Eric Banks
Roger Zurawicki
Andrey Sivachenko
Ryan Poplin
Guillermo del Angel