d59e6ed274
Fix for RefSeqCodec bug and better error messages
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-- RefSeqCodec bug: getFeatureClass() returned RefSeqCodec.class, not RefSeqFeature.class. Really should change this in Tribble to require Class<T extends Feature> to get compile time type checking
-- Better error messages that actually list the available tribble types, when there's a type error
2011-08-17 16:22:07 -04:00
53006da9a5
Improved descriptions for the SnpEff annotations in the VCF header
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(based on Eric's feedback).
2011-08-17 16:09:10 -04:00
784fb148b9
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-17 15:47:01 -04:00
671330950d
Updated Beagle walker for gatkdocs format. Pushed unsupported, undocumented arguments to @Hidden
2011-08-17 15:46:31 -04:00
0af68e052a
Merge branch 'master' of ssh://cga1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-17 15:17:47 -04:00
a423546cdd
fix: RefSeq contains records with zero coding length and the refsec codec/feature used to crash on those; now such records are ignored, with warning printed (once)
2011-08-17 15:17:31 -04:00
710d34633e
now the reads that are too long are truly ignored (fix of the fix)
2011-08-17 15:16:23 -04:00
40f64a27be
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-17 14:21:55 -04:00
2f19046f0c
Adding docs to the 2 beasts. Saved the worst for last.
2011-08-17 14:19:14 -04:00
8a92143938
Change @argument to @input
2011-08-17 14:18:34 -04:00
4dab59bfb5
Added: a simulator for intron loss reads.
2011-08-17 14:14:31 -04:00
eea8087c73
Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-17 14:06:25 -04:00
069554efe5
somatic indel detector does not die on reads that are too long (likely contain a huge deletion) anymore; instead print a warning and ignore the read
2011-08-17 14:05:19 -04:00
c405a75f54
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-17 13:28:25 -04:00
575303ae6b
Renaming for consistency and bringing up to speed with new rod system
2011-08-17 13:28:19 -04:00
6d629c176c
Adding docs
2011-08-17 13:27:36 -04:00
a21e193a9e
Adding docs to 3 more walkers
2011-08-17 12:35:08 -04:00
98acb546a9
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-17 12:22:29 -04:00
d1bb302d12
Added GatkDocs documentation
2011-08-17 12:21:37 -04:00
3da71a9bb6
Clean up summary
2011-08-17 12:04:45 -04:00
c6fb215faf
GATKDocs for VariantsToTable
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-- Made a previously required argument optional, as this was a long-standing bug
2011-08-17 12:02:41 -04:00
5f794d16a7
Fixed bad character in documentation
2011-08-17 12:01:08 -04:00
9d1d5bd27a
Revert "Fixed bad character in documentation"
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This reverts commit a1f50c82d3cb25e5e83d36e9054d74cdee957d87.
2011-08-17 11:57:31 -04:00
78deb3f195
Fixed bad character in documentation
2011-08-17 11:57:00 -04:00
79dcfca25f
Fixed bad character in documentation
2011-08-17 11:56:51 -04:00
c365da3c51
Fixed final old rodBinding from PipelineTest
2011-08-17 11:56:30 -04:00
b3b5d608ca
Adding docs to yet more walkers
2011-08-17 09:57:19 -04:00
fadcbf68fd
Adding docs to QC walkers
2011-08-17 09:39:33 -04:00
5f3f46aad1
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-16 16:26:33 -04:00
946f5c53fe
Adding docs to more walkers
2011-08-16 16:26:26 -04:00
6e828260a0
Removed -B support. Now explodes with error if -B provided.
2011-08-16 16:13:47 -04:00
0c3466d2c3
typo
2011-08-16 15:25:35 -04:00
008aa281e7
add interval list
2011-08-16 15:24:05 -04:00
7cb42efccb
Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-16 15:23:13 -04:00
99e7e53744
script it
2011-08-16 14:37:49 -04:00
b36b047eb8
val --> var
2011-08-16 14:36:09 -04:00
edd39da2ea
Merge branch 'master' of ssh://gsa2/humgen/gsa-scr1/chartl/dev/git
2011-08-16 14:32:48 -04:00
880de6ccb0
RFCombine alteration
2011-08-16 14:32:06 -04:00
632cd9bed1
script to scatter-gather left align variants
2011-08-16 14:31:12 -04:00
2d5bbecd9e
Merged bug fix from Stable into Unstable
2011-08-16 14:19:04 -04:00
9d4add3268
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-08-16 14:18:03 -04:00
170d1ff7b6
Fix in UG for trying to call indels at IUPAC code bases when in EMIT_ALL_SITES mode
2011-08-16 14:17:46 -04:00
9f3328db53
fixing read group name collision: before writing the read into respective stream in nway-out mode we now retrieve the original rg, not the merged/modified one
2011-08-16 13:45:40 -04:00
a684233265
Merge branch 'master' of ssh://cga1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-16 13:40:59 -04:00
c71a4e1832
this is a bug fix; reverting in unstable and pushing from stable instead
2011-08-16 13:40:35 -04:00
801659c1d7
Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-16 13:24:51 -04:00
637f3e0756
Commenting out the @Argument so queue will build -- still unsure where the bug is, but this walker can't be brought properly onto the new ROD system yet
2011-08-16 13:24:30 -04:00
335421820e
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-16 13:08:25 -04:00
ab0b56ed11
Minor doc fixes
2011-08-16 12:55:45 -04:00
125ad0bcfa
Added docs to RTC
2011-08-16 12:46:48 -04:00
Mark DePristo
David Roazen
Guillermo del Angel
Andrey Sivachenko
Eric Banks
Chris Hartl
Menachem Fromer
Ryan Poplin