gatk3的最后一个经典版本3.8

Go to file

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
licensing	deleted old license files	2013-07-02 16:36:47 -04:00
protected	create a new read transformer that refactor NDN cigar elements to one N element.	2014-04-28 11:29:00 -04:00
public	create a new read transformer that refactor NDN cigar elements to one N element.	2014-04-28 11:29:00 -04:00
settings/helpTemplates	Replaced local drmaa and Jama artifacts with versions from maven central.	2014-02-22 01:21:35 +08:00
.gitignore	Fixed bug using GraphBased due to infinite likelihoods resulting from the calculation of alignment cost of very long insertion or deletions (done in linear scale)	2014-04-01 16:14:52 -04:00
README.md	Update README file for the 2.6 release	2013-06-20 13:08:29 -04:00
ant-bridge.sh	Rename existing PipelineTests to QueueTests to prepare for upcoming push of new pipeline tests	2014-03-10 21:24:03 -04:00
intellij_example.tar.bz2	Removed the intellij files from the root and made an example package for new users. This allows users to start at the same page and then change it as they see fit without interfering with the repo (thanks guillermo!)	2012-09-27 11:04:56 -04:00
pom.xml	Quoting -out parameter during resource bundle (StingText.properties) creation.	2014-04-15 17:06:49 +08:00

README.md

The Genome Analysis Toolkit

See http://www.broadinstitute.org/gatk/