be2d29ce69
Final PED documentation
2011-10-05 15:17:41 -07:00
3226d5dc0d
Merge branch 'master' into ped
2011-10-05 15:03:09 -07:00
6a573437af
Details documentation arguments for -ped
2011-10-05 15:00:58 -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
a45d985818
TODO method stubs
2011-10-04 15:54:09 -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
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
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
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
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
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
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
Mark DePristo
Mauricio Carneiro
Eric Banks
Roger Zurawicki
Andrey Sivachenko
Ryan Poplin