zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
gatk-3.8/public/java/test/org/broadinstitute/sting
History
Geraldine Van der Auwera edf5880022 Updated SAMPileup codec and pileup-related docs 
Problem: the codec was written to take in consensus pileups produced with pileup -c option (which consists of 10 or 13 fields per line depending on the variant type) but errored out on the basic pileup format (which only has 6 fields per line). This was inconsistent and confusing to users.

	Solution: I added a switch in the parsing to recognize and handle both cases more appropriately, and updated related docs. While I was at it I also improved error messages in CheckPileup, which now emits User Error: Bad Input exceptions when reporting mismatches. Which may not be the best thing to do (ultimately they're not really errors, they're just reporting unwelcome results) but it beats emitting Runtime Exceptions.

	Tested by CheckPileupIntegrationTest which tests both format cases.
 		2014-01-14 09:14:16 -05:00
..
commandline Adding the functionality to enable users to input a file of VCFs for -V. 2014-01-08 00:45:00 -05:00
gatk Updated SAMPileup codec and pileup-related docs 2014-01-14 09:14:16 -05:00
jna Fix pipeline tests that were not respecting the pipeline test dry run setting 2013-06-28 15:27:17 -04:00
utils Added some bug fixes to the gVCF merging code after finally getting some real data to play with. 2014-01-08 08:34:35 -05:00
BaseTest.java Adding Graph-based likelihood ratio calculation to HC 2013-12-02 19:37:19 -05:00
ExampleToCopyUnitTest.java Add a class-based DataProvider 2013-12-03 13:31:01 -05:00
MD5DB.java Enable convenient display of diff engine output in Bamboo, plus misc. minor test-related improvements 2013-05-10 19:00:33 -04:00
MD5Mismatch.java Enable convenient display of diff engine output in Bamboo, plus misc. minor test-related improvements 2013-05-10 19:00:33 -04:00
StingTextReporter.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
TestNGTestTransformer.java Adding Graph-based likelihood ratio calculation to HC 2013-12-02 19:37:19 -05:00
WalkerTest.java Throw a GVCFIndexException when the user doesn't specify the optimal indexing strategy 2013-12-03 23:12:14 -05:00