zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
gatk-3.8/public
History
Alec Wysoker 0369f93b24 GATK changes to conform to Tribble refactoring as part improving Tabix support in Tribble (among other things). 
1. Enable on-the-fly indexing for vcf.gz.
2. Handle on-the-fly indexing where file to be indexed is not a regular file, thus index should not be created.
3. Add method setProgressLogger to all SAMFileWriter implementations.
4. Revved picard to 1.109.1722
5. IndelRealigner md5s change because the MC tag is added to records now.

Fixed up and signed off by ebanks.
 		2014-03-17 11:56:22 -04:00
..
VectorPairHMM Removed g_haplotype* global variables in native code so that it works 2014-03-06 22:08:35 -08:00
c At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings. 2012-01-17 14:47:53 -05:00
chainFiles
…
doc Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs) 2013-03-12 10:57:14 -04:00
external-example Update pom versions to mark the start of GATK 3.1 development 2014-03-06 00:05:58 -05:00
gatk-framework GATK changes to conform to Tribble refactoring as part improving Tabix support in Tribble (among other things). 2014-03-17 11:56:22 -04:00
gatk-package Unconditionally include all of commons-httpclient in the GATK/Queue jars 2014-03-14 10:50:15 -04:00
gatk-queue-extgen Update pom versions to mark the start of GATK 3.1 development 2014-03-06 00:05:58 -05:00
gsalib Update pom versions to mark the start of GATK 3.1 development 2014-03-06 00:05:58 -05:00
java/config Moved files to maven directories. 2014-02-03 13:50:44 -05:00
package-tests Rename existing PipelineTests to QueueTests to prepare for upcoming push of new pipeline tests 2014-03-10 21:24:03 -04:00
perl Fixing the liftover script to not require strict VCF header validation. 2013-11-07 09:02:17 -05:00
queue-framework Rename existing PipelineTests to QueueTests to prepare for upcoming push of new pipeline tests 2014-03-10 21:24:03 -04:00
queue-package Unconditionally include all of commons-httpclient in the GATK/Queue jars 2014-03-14 10:50:15 -04:00
repo GATK changes to conform to Tribble refactoring as part improving Tabix support in Tribble (among other things). 2014-03-17 11:56:22 -04:00
sting-root GATK changes to conform to Tribble refactoring as part improving Tabix support in Tribble (among other things). 2014-03-17 11:56:22 -04:00
sting-utils Merge remote-tracking branch 'origin/master' into intel 2014-03-10 14:07:36 -04:00
pom.xml Rename existing PipelineTests to QueueTests to prepare for upcoming push of new pipeline tests 2014-03-10 21:24:03 -04:00