gatk-3.8

Author	SHA1	Message	Date
Ami Levy-Moonshine	b4447cdca2	In cases where one uses VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE we used to verify that the samples names are unique in VariantContextUtils.simpleMerge for each VCs. It couse to a bug that was reported on the forum (when a VCs had 2 VC from the same sample). Now we will check it only in CombineVariants.init using the headers. A new function was added to SamplesUtils with unitTests in CVunitTest.java.	2013-01-25 15:49:51 -05:00
Mauricio Carneiro	2a4ccfe6fd	Updated all JAVA file licenses accordingly GSATDG-5	2013-01-10 17:06:41 -05:00
David Roazen	07b369ca7e	Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package This is an intermediate commit so that there is a record of these changes in our commit history. Next step is to isolate the test classes as well, and then move the entire package to the Picard repository and replace it with a jar in our repo. -Removed all dependencies on org.broadinstitute.sting (still need to do the test classes, though) -Had to split some of the utility classes into "GATK-specific" vs generic methods (eg., GATKVCFUtils vs. VCFUtils) -Placement of some methods and choice of exception classes to replace the StingExceptions and UserExceptions may need to be tweaked until everyone is happy, but this can be done after the move.	2012-12-19 10:25:22 -05:00

Author

SHA1

Message

Date

Ami Levy-Moonshine

In cases where one uses VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE we used to verify that the samples names are unique in VariantContextUtils.simpleMerge for each VCs. It couse to a bug that was reported on the forum (when a VCs had 2 VC from the same sample).

Now we will check it only in CombineVariants.init using the headers. A new function was added to SamplesUtils with unitTests in CVunitTest.java.

2013-01-25 15:49:51 -05:00

Mauricio Carneiro

2a4ccfe6fd

Updated all JAVA file licenses accordingly

GSATDG-5

2013-01-10 17:06:41 -05:00

David Roazen

07b369ca7e

Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package

This is an intermediate commit so that there is a record of these changes in our
commit history. Next step is to isolate the test classes as well, and then move
the entire package to the Picard repository and replace it with a jar in our repo.

-Removed all dependencies on org.broadinstitute.sting (still need to do the test classes,
though)

-Had to split some of the utility classes into "GATK-specific" vs generic methods
(eg., GATKVCFUtils vs. VCFUtils)

-Placement of some methods and choice of exception classes to replace the StingExceptions
and UserExceptions may need to be tweaked until everyone is happy, but this can be
done after the move.

2012-12-19 10:25:22 -05:00

3 Commits (b4447cdca2fb6c791f5fbea93e898e96a8b5d0d2)