73f9d1f217
GATK read group requirement iron hand
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-- The GATK will now throw a user exception if it opens a SAM/BAM file that doesn't have at least one RG defined
-- LIBS again throws an error if the complete list of samples isn't provided
-- Updating ExmpleCountLociPipeline test to use the well-formated versions of the exampleBAM and exampleFASTA files in testdata, instead of the old broken ones in validation_data.
-- Convenience constructors for UserExceptions.MalformedBAM
2011-10-06 08:40:35 -07:00
23845ac798
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-06 08:17:08 -07:00
4b5b9155a9
Fixed bad expected value in PedReaderUnitTest
2011-10-06 08:16:47 -07:00
daa5999489
Fixed typo in argument description
2011-10-06 08:16:25 -07:00
c649759978
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-06 10:10:46 -04:00
2f12bfaad5
Merged bug fix from Stable into Unstable
2011-10-06 10:10:00 -04:00
efca1fdfd8
Revert change until I figure out how to use classfileset/rootfileset
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with a vanilla ant install.
This reverts commit 4c9022872beec8dc0700a1320a267e3603c8212d.
2011-10-06 10:08:48 -04:00
8a474e38ff
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-06 10:08:39 -04:00
93f7e632bd
Minor fix/enhancement for VariantEval: if a vcf has symbolic alleles, program would crash ungracefully - now we'll just skip record without processing. This is a big issue since we can't process 1000G integration files with code as is.
2011-10-06 10:07:46 -04:00
190be4d0d1
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-05 21:27:11 -07:00
8e6845806a
Allowing empty samples list in LIBS
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-- Right now we cannot process BAM files without read groups because we enforce the samples list to not be empty when there's a SAM record. Now if there are reads and there are no samples we add the "null" sample so that LIBS walks the reads properly
2011-10-05 21:26:21 -07:00
a3c5a31686
Oops, forgot the PED test file
2011-10-05 21:09:08 -07:00
180c8f286f
Merged bug fix from Stable into Unstable
2011-10-05 20:37:43 -04:00
55b9f06527
Ensure that IndelRealigner n-way out option supports MD5 generation.
2011-10-05 20:36:28 -04:00
b945e97de1
Shouldn't have committed the non-fetching version by default
2011-10-05 17:12:48 -07:00
b068846407
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-05 17:12:09 -07:00
6d6149b9a2
Updated gsalib gsa.read.gatkreport to return all reports, even those beginning with '.'.
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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
982983355f
Merged bug fix from Stable into Unstable
2011-10-05 18:27:29 -04:00
dd780dba5f
Rather than just picking a few classes to be the roots of the vcf jar and
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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
a91509e7dd
Shouldn't be public
2011-10-05 15:22:57 -07:00
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
dc6d71dec5
Merged bug fix from Stable into Unstable
2011-10-05 16:53:32 -04:00
b732f740d2
Revert "Change vcf jar to use a classfileset to pull all dependencies. Should save"
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This reverts commit 441022c4c600624928da46419a6a289200700f3e.
2011-10-05 16:51:30 -04:00
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
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
Mark DePristo
Guillermo del Angel
Matt Hanna
Khalid Shakir
David Roazen
Mauricio Carneiro
Eric Banks