zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
gatk-3.8/public
History
Ami Levy-Moonshine 13dd755468 create a new read transformer that refactor NDN cigar elements to one N element. 
story:
https://www.pivotaltracker.com/story/show/69648104

description:
This read transformer will refactor cigar strings that contain N-D-N elements to one N element (with total length of the three refactored elements).
This is intended primarily for users of RNA-Seq data handling programs such as TopHat2.
Currently we consider that the internal N-D-N motif is illegal and we error out when we encounter it. By refactoring the cigar string of
those specific reads, users of TopHat and other tools can circumvent this problem without affecting the rest of their dataset.

edit: address review comments - change the tool's name and change the tool to be a readTransformer instead of read filter
 		2014-04-28 11:29:00 -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 The contig is named MT not M in b36. Delivers PT68890442. 2014-04-08 10:03:47 -04:00
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 3.2 development 2014-03-18 01:18:59 -04:00
gatk-framework create a new read transformer that refactor NDN cigar elements to one N element. 2014-04-28 11:29:00 -04:00
gatk-package Update pom versions to mark the start of GATK 3.2 development 2014-03-18 01:18:59 -04:00
gatk-queue-extgen Update pom versions to mark the start of GATK 3.2 development 2014-03-18 01:18:59 -04:00
gsalib Update pom versions to mark the start of GATK 3.2 development 2014-03-18 01:18:59 -04:00
java/config Moved files to maven directories. 2014-02-03 13:50:44 -05:00
package-tests Update pom versions to mark the start of GATK 3.2 development 2014-03-18 01:18:59 -04:00
perl Fixing the liftover script to not require strict VCF header validation. 2013-11-07 09:02:17 -05:00
queue-framework Update pom versions to mark the start of GATK 3.2 development 2014-03-18 01:18:59 -04:00
queue-package Update pom versions to mark the start of GATK 3.2 development 2014-03-18 01:18:59 -04:00
repo Rev Picard 1.111.1920 2014-04-16 14:39:19 -04:00
sting-root Rev Picard 1.111.1920 2014-04-16 14:39:19 -04:00
sting-utils Update pom versions to mark the start of GATK 3.2 development 2014-03-18 01:18:59 -04:00
pom.xml Update pom versions to mark the start of GATK 3.2 development 2014-03-18 01:18:59 -04:00