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
Mark DePristo 5b0ade67c8 Updates to VCF processing for better BCF processing 
-- getMetaData now split into getMetaDataInSortedOrder() [old functionality] and getMetaDataInOriginalOrder() [according to the header order].  Important as BCF uses the order of elements in the header in the offsets to keys, and we were automatically sorting the BCF2 header which is out of order in samtools and the whole system was going crazy
-- Updating GATK code to use the appropriate header function (this is why so many files have changed)
-- BCF2 code was busted in not differentiating PASS from . from FILTER in VC (tests coming that will actually stress this)
-- Bugfix for adding contig lines to BCF2 header dictionary
-- VCFHeader metaData no longer sorted internally.  The system now maintains the data in header order, and only sorts output as requested in API
-- VCFWriter and BCF2Writer now explictly sort their header lines
-- Don't allow filters to be added that are PASS in the contract
 		2012-07-08 15:44:33 -07:00
..
alignment Reinitialize random seed in the bwa bindings from the fixed seed stored in the 2011-07-22 13:41:53 -04:00
commandline Cleanup of VCF header lines and constants, BCF2 bugfixes 2012-06-21 15:16:31 -04:00
gatk Adding the model name to the VQSR filter lines so that they don't get clobbered with consecutive VQSR runs for SNPs and then indels. 2012-07-03 14:30:37 -04:00
jna Updated hard limit MathUtils.MAXN number of samples from 11,000 to 50,000. 2012-05-29 11:18:22 -04:00
utils Updates to VCF processing for better BCF processing 2012-07-08 15:44:33 -07:00
BaseTest.java BCF2 with support symbolic alleles 2012-06-30 11:22:48 -04:00
MD5DB.java Finalizing BCF2 mark III commit 2012-06-21 15:16:27 -04:00
MD5Mismatch.java Final updates to integration tests for BCF2 2012-05-24 10:58:59 -04:00
StingTextReporter.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
WalkerTest.java Disable shadowBCF for VariantRecalibrationWalkers tests because it cannot handle symbolic alleles yet 2012-06-26 15:28:32 -04:00