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
625ffb6a07
LocusIteratorByState and ReadBackedPileups no long use Sample
2011-09-29 14:52:11 -04:00
b3a2371925
Merge branch 'master' into ped
2011-09-29 14:32:17 -04:00
68761a6e28
Removed sample from header
2011-09-29 14:13:05 -04:00
a5e75cd14c
Outputting both consensus base qualities and counts
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The base qualities of a consensus reads are now the average quality of the bases forming the consensus base (most common base) and the consensus quality tag now carry an array with the counts of each base in the consensus. This should increase file size but improve calling sensitivity/specificity.
2011-09-29 12:54:41 -04:00
d62f2f33bc
Added indel specific context size parameter
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Parameter was added to the framework but implementing the functionality is pending.
2011-09-29 12:54:41 -04:00
505416b6c0
Merge branch 'master' into ped
2011-09-29 12:22:39 -04:00
21c4abdd36
Disabling all SlidingReadUnitTests
2011-09-29 12:20:35 -04:00
4086fa768f
Disabling all ReadClipperUnitTests
2011-09-29 12:20:35 -04:00
9536845e35
Cleaning up unused code in MV
2011-09-29 12:20:07 -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
6dec932ca9
Merge branch 'master' of ssh://gsa3.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-29 11:47:13 -04:00
c08468eb9d
A couple of updates while trying to get desired R 2.13 compactPDF support.
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preQC:
- For R 2.13 when parsing fingerprints explicitly coercing the text before parsing
- Added LOD geom_line() at +/-3 based on Tim's presentation at PM meeting (ppt to go to pipeline wiki asap)
- PF_INDEL_RATE of zero replaced with NA
- NA's are not "violations" auto filter samples since 0+NA = NA, and subset test only looks for 0 violations
- Restored plots for MEAN_READ_LENGTH, BAD_CYCLES, and MEDIAN_INSERT_SIZE by explicitly print()'ing the created plots
postQC:
- Fixed R 2.13 font scaling by moving size out of aes, except when using highlighting
- TODO: Don't know how to scale by aes for highlighting *and* use a smaller overall font size outside aes
2011-09-29 11:21:50 -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
e197dcd1f3
Pre-cleanup commit of Sample and SampleDataSource
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-- SampleDataSource has all reader functionality disabled
2011-09-29 09:44:18 -04:00
4d31673cc5
No longer supporting YAML file allows us to delete 75% of the sample's codebase
2011-09-29 09:43:31 -04:00
e366ee18bc
Adding ability to read in and make use of kmer quality tables during HMM evaluation
2011-09-29 07:46:19 -04:00
9e32ede5b2
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-29 07:40:08 -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
f49a12de6b
Updating latest changes from the repository to reduce reads repo
2011-09-28 22:31:57 -04:00
Andrey Sivachenko
Mark DePristo
Mauricio Carneiro
Ryan Poplin
Guillermo del Angel
Khalid Shakir
Roger Zurawicki