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
36daaa7bda
Extract GA, AR2, and DR2 from the BEAGLE output
2011-07-26 17:29:23 -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
5136eea7be
Merge branch 'desktop'
2011-07-25 15:02:42 -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
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
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
987e889137
Merge branch 'desktop'
2011-07-25 11:50:15 -04:00
0eecda6be4
Forgot to toggle switch state when genotypes are first seen in a reversed or consistent phase.
2011-07-25 11:50:02 -04:00
357f503a21
Merge branch 'desktop'
2011-07-25 11:36:27 -04:00
6389b29c4f
Computes the switch error rate for many samples at a time.
2011-07-25 11:36:08 -04:00
0b43ee117c
Added the required=false tag to the -noST and -noEV arguments so the auto-help output doesn't look weird (i.e. listing arguments as required when their value has already been specified by default).
2011-07-25 11:35:34 -04:00
bbb8473f03
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-25 10:59:00 -04:00
5db05d2873
Refactored Mills codecs so that they're in correct packages
2011-07-25 10:25:25 -04:00
115879b31f
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-25 10:13:16 -04:00
4c6c16f895
Documented following the new gatkdoc framework
2011-07-25 00:25:08 -04:00
2039ce6102
Default values now displayed in arguments
...
DiffEngine fixed so that newInstance() would work. Pretty quickly encountered a situation where newInstance() failed. Debug output now written when this occurs in the log.
Logger now used instead of standard out, with INFO the default level.
2011-07-24 22:56:55 -04:00
c43b5981f2
Hidden variables are hidden by default. Settable by command line option
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DiffObjectsWalker test arguments removed.
Minor refactoring of GATKDoclet
2011-07-24 20:52:44 -04:00
1c1f1da349
Fixing compilation
2011-07-24 20:01:59 -04:00
9f06f6c493
Split GATKDoclet from ResourceBundleDoclet. Refactored GaTKDocWorkUnit
2011-07-24 20:00:04 -04:00
e602166f78
First fully functional version outputting a full vcf
2011-07-24 19:38:59 -04:00
7b84347047
Main index is sorted by the template now.
2011-07-24 18:19:40 -04:00
ff85687679
Merge branch 'master' into help
2011-07-24 18:14:32 -04:00
83996f7951
Enumerated types are working.
2011-07-24 18:14:21 -04:00
3c34e9fa65
Cleanup emuns and tables
2011-07-24 17:45:58 -04:00
c620d96c96
Inline enum documentation is working
2011-07-24 17:22:14 -04:00
793e7d3d1d
Improved header and argument details
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Argument detail structure cleaned up. Only relevant pieces of information are shown now, and in a cleaner layout.
Misc. cleanup in the code.
2011-07-24 16:36:25 -04:00
c6af4efcdc
Implemented see also and version header
2011-07-24 16:10:17 -04:00
b8db0510e0
Sytle sheet and common functions
2011-07-24 15:43:23 -04:00
5e0fe2d0f9
Support for style.css via refactored common.html included in all files
2011-07-24 15:42:39 -04:00
d0ab6bf7a9
Now links to sub and superclass documentation, where possible.
2011-07-24 09:56:17 -04:00
e2dabb70b8
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-24 08:57:47 -04:00
1ef964c92c
Merge branch 'contig'
2011-07-24 02:40:42 -04:00
e0cb403b33
A read walker for contig statistics
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I used this walker for my mtdna analysis where the goal was to see how the chromosomes were represented by the sequences in the bam files. It is very useful as a first look at a new dataset if you want to have an idea of where most of the reads fall. It reports the number of reads in each contig, percetages, enrichment as well as the expected number of reads for each contig and enrichment given the size of your dataset. I will document it accordingly with the new documentation tool. It's in public, and I'm happy to support it.
2011-07-24 02:36:17 -04:00
Kiran V Garimella
Guillermo del Angel
Mauricio Carneiro
Mark DePristo