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
9dfb57168a
RodBinding source is no longer assumed to be a file
2011-07-26 13:59:44 -04:00
d0badd5bd6
RodBinding subclassed to VariantContextRodBinding for easy access to VariantContext providing RODs
2011-07-26 13:54:55 -04:00
7ab8b53339
Support for List<RodBinding> argument type
2011-07-26 11:37:31 -04:00
38969b9783
Prototype of RODBinding @Arguments instead of -B syntax
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Initial version of RodBinding class.
Flow from walker Rodbinding @Arguments -> RMDTriplet (old system) -> GATK engine (standard). Will need refactoring.
2011-07-26 11:09:06 -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
a53aeb75ab
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-25 15:10:35 -04:00
a29554e565
Removing the Genomic Annotator and its supporting classes
2011-07-25 15:10:25 -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
b11765b360
Merge branch 'desktop'
2011-07-25 13:53:43 -04:00
a0dd166364
Print metrics for both the unphased and rbp-phased data for easier comparison.
2011-07-25 13:53:33 -04:00
2a51543693
Actually should have been gone...
2011-07-25 13:27:42 -04:00
ebfd8df06c
Restoring accidentially deleted unit test
2011-07-25 13:25:30 -04:00
f3049fba63
refdata directory cleanup
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Removing unused files RODRecordIterator, ReferenceOrderedData, QueryableTrack, RMDTrackCreationException, GATKFeatureIterator, ReferenceOrderedDataUnitTest
Refactored dbSNP and refseq utilities to be closer to the other files implementing these features
2011-07-25 13:21:52 -04:00
8014fad6ff
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-25 13:20:44 -04:00
2ac490dbdf
Fix improper detection of command-line arguments with missing values.
2011-07-25 13:20:00 -04:00
ac5a11b4f3
Merge branch 'desktop'
2011-07-25 13:18:41 -04:00
62011403b0
Constrains evaluation to places where both the unphased and rbp-phased data show the same genotype.
2011-07-25 13:00:29 -04:00
90947ab359
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-25 12:53:56 -04:00
44bd9ae703
Restoring UninstantiableWalker, as it is not going to be possible to run ant test; ant gatkdocs without ant clean in between
2011-07-25 12:53:06 -04:00
Mauricio Carneiro
Kiran V Garimella
Mark DePristo
Matt Hanna
Eric Banks