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
...
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
...
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
...
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
acda8eb09c
Commented out test that causes new CommandLineGATK() to fail
2011-07-25 12:43:27 -04:00
95b48eface
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable into repval
2011-07-25 12:09:09 -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
1a268ff1fd
Refactor so that GenotypeAnnotation and InfoFieldAnnotation share common superclass VariantAnnotatorAnnotation
2011-07-25 10:55:09 -04:00
7f8e6a97ee
InfoFieldAnnotation now an abstract class extended by annotations so doc system works
2011-07-25 10:47:11 -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
Kiran V Garimella
Matt Hanna
Eric Banks
Mark DePristo
Mauricio Carneiro
Guillermo del Angel