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
David Roazen 51ec5404d4 SAMDataSource: always consolidate cigar strings into canonical form 
-Collapses zero-length and repeated cigar elements, neither of which
 can necessarily be handled correctly by downstream code (like LIBS).

-Consolidation is done before read filters, because not all read filters
 behave correctly with non-consoliated cigars.

-Examined other uses of consolidateCigar() throughout the GATK, and
 found them to not be redundant with the new engine-level consolidation
 (they're all on artificially-created cigars in the HaplotypeCaller
 and SmithWaterman classes)

-Improved comments in SAMDataSource.applyDecoratingIterators()

-Updated MD5s; differences were examined and found to be innocuous

-Two tests: -Unit test for ReadFormattingIterator
            -Integration test for correct handling of zero-length
             cigar elements by the GATK engine as a whole
 		2013-06-19 13:29:01 -04:00
..
commandline Fixed the logic of the @Output annotation and its interaction with 'required'. 2013-03-14 11:58:51 -04:00
gatk SAMDataSource: always consolidate cigar strings into canonical form 2013-06-19 13:29:01 -04:00
jna Fix more tests that fail when run in parallel on the farm 2013-03-12 16:53:30 -04:00
utils Add genotyping accuracy assessment to AssessNA12878 2013-06-13 15:05:32 -04:00
BaseTest.java Replace org.broadinstitute.variant with jar built from the Picard repo 2013-02-05 17:24:25 -05:00
ExampleToCopyUnitTest.java Replace org.broadinstitute.variant with jar built from the Picard repo 2013-02-05 17:24:25 -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 Fix tests that were consistently or intermittently failing when run in parallel on the farm 2013-03-06 13:56:54 -05:00
WalkerTest.java Reduce number of leftover temp files in GATK runs 2013-06-14 15:56:03 -04:00