e7b4959ebe
Merged bug fix from Stable into Unstable
2011-07-30 02:06:45 -04:00
2d94037ad0
Remove temporary index files (*.bai)
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some temporary index files were not being removed.
2011-07-30 02:05:22 -04:00
b06deac9ea
Merged bug fix from Stable into Unstable
2011-07-29 10:02:36 -04:00
c0d4110ffd
Correcting redundant warning text.
2011-07-29 10:01:11 -04:00
7a2a65155f
Merged bug fix from Stable into Unstable
2011-07-28 13:56:43 -04:00
1afc49a297
There are some really 'interesting' (but apparently valid) records in the Mus musculus dbSNP file. Generalized the handling of complex cases in the dbSNP adaptor to handle it all. I just grabbed the actual Mus musculus dbSNP file as a test, ran it whole genome, and confirmed that we finally produce a valid VCF on it. Should be the last commit needed on this adaptor.
2011-07-28 13:55:58 -04:00
1865211b6d
Merged bug fix from Stable into Unstable
2011-07-27 22:52:06 -04:00
6230315ff2
Along with my half-written commit message from earlier, I also forgot to commit the integration test updates. This is what happens when you try to do things 30 seconds before you leave for the day. To finish up from before: complex events weren't being padded with the reference base as per the VCF spec. They are now.
2011-07-27 22:51:21 -04:00
5809a61b20
Merged bug fix from Stable into Unstable
2011-07-27 16:14:59 -04:00
64aad67b5f
Fixing dbSNP adaptor for complex indels (wasn)
2011-07-27 16:13:45 -04:00
ab69b8e4ee
Merged bug fix from Stable into Unstable
2011-07-27 12:37:34 -04:00
6ebd83478b
Fixed build.xml to reflect path changes for gsalib
2011-07-27 12:37:00 -04:00
fe52f2dd8c
Merged bug fix from Stable into Unstable
2011-07-27 12:30:15 -04:00
ca35defdcd
Moved gsalib sources from private/ to public/
2011-07-27 12:29:43 -04:00
ada2f21976
Revert "Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable"
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This reverts commit 9c81ef835a3ac581d4eb9cf1243e30df20a46795, reversing
changes made to f23d3ad5aec1c70cc1ecc48b295258aa70d30c7d.
2011-07-27 12:27:17 -04:00
86d38b7f0b
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-27 10:35:19 -04:00
dc8061e7a6
Moved gsalib from private/ to public/
2011-07-27 10:34:56 -04:00
e607461db1
leftover </ol> removed...
2011-07-26 19:31:33 -04:00
20a3b31b61
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-26 19:29:45 -04:00
321afac4e8
Updates to the help layout.
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*New style.css, new template for the walker auto-generated html. Short description is no longer repeated in the long description of the walker.
*Updated DiffObjectsWalker and ContigStatsWalker as "reference" documented walkers.
2011-07-26 19:29:25 -04:00
405e521d44
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-26 17:56:48 -04:00
92a11ed8dc
Updated MD5 for PhaseByTransmissionIntegrationTest
2011-07-26 17:52:25 -04:00
412c466de6
Bug fix, wherein triple-hets after genotype refinement need to be left unphased, not just prior to refinement
2011-07-26 17:43:43 -04:00
81f8e05bfa
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-26 17:35:46 -04:00
f6a5e0e36a
Go for global integrationtest path first, if possible.
2011-07-26 17:35:30 -04:00
36daaa7bda
Extract GA, AR2, and DR2 from the BEAGLE output
2011-07-26 17:29:23 -04:00
fec495e292
Fix a nasty little bug in the sharding system: if the last shard in contig n
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overlaps exactly on disk with the first shard in contig n+1, the shards
would be merged together to avoid duplicate extraction. Unfortunately,
the interval overlap filter couldn't handle shards spanning contigs, and
was choosing to filter out reads from contig n+1 which should have been
included.
I'm not completely sure why the BAM indexing code would ever specify that the
end of one chromosome had the same on-disk location as the start of the next
one. I suspect that this is a indexer performance bug.
2011-07-26 15:43:20 -04:00
d87e6bdea0
Don't process sites where everyone is hom-ref, and print no-call genotypes when necessary
2011-07-26 08:44:27 -04:00
4e09f87dfa
Debug: fixed bug where position wasn't output. Experimenting with allele and genotype printing
2011-07-26 01:44:19 -04:00
075f7683b2
Debug: fixed some typos that ended up referring to the wrong VCs when populating table
2011-07-26 01:31:11 -04:00
b51d461d09
Debug: declared missing AF columns
2011-07-26 01:23:15 -04:00
2d86c0d7d4
Debug: get all attributes as raw Object types, rather than as specific types
2011-07-26 01:19:30 -04:00
a615556781
Debug: removed restrictions that all VCs had to be non-null
2011-07-26 01:13:33 -04:00
ef4101b62d
Merge branch 'desktop'
2011-07-25 17:38:03 -04:00
70b69d8e89
Fixed a typo - should all set(), not addColumn()
2011-07-25 17:37:14 -04:00
5854a56366
Merge branch 'desktop'
2011-07-25 17:20:43 -04:00
626552481f
Check if the tracker is null and, if so, do not process the locus.
2011-07-25 17:20:36 -04:00
3361b46add
Merge branch 'desktop'
2011-07-25 16:51:29 -04:00
edaa0c5d7f
One-off walker to take a whole bunch of RBP-analysis VCFs and dump them to an R-readable table
2011-07-25 16:40:16 -04:00
088fc39308
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-25 15:54:56 -04:00
6fd6684e86
Merged bug fix from Stable into Unstable
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Conflicts:
build.xml
2011-07-25 15:21:17 -04:00
6f43284053
Switch to including our entire exception tree rather than just UserException.
2011-07-25 15:19:41 -04:00
5136eea7be
Merge branch 'desktop'
2011-07-25 15:02:42 -04:00
3afcb3415d
Max of 1000 records will be loaded and compared to avoid heap size problem.
2011-07-25 14:58:31 -04:00
504b3ef5ef
Removed constraint to only evaluate eval and comp tracks at sites where genotypes match.
2011-07-25 14:58:10 -04:00
af0b5883c3
In unstable, add a reference to DocumentedGATKFeature to vcf.jar, which is now
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a static dependency of UserExceptions.
2011-07-25 14:36:12 -04:00
6c49197de6
Merged bug fix from Stable into Unstable
2011-07-25 14:32:33 -04:00
a00e302321
Fix formatting issue.
2011-07-25 14:31:40 -04:00
29c08ac3c6
Merge branch 'desktop'
2011-07-25 14:06:52 -04:00
a2d280b85e
Forgot to change the name of the switchState columns
2011-07-25 14:06:41 -04:00
Mauricio Carneiro
Ryan Poplin
Eric Banks
Kiran V Garimella
Mark DePristo
Matt Hanna