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
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gatk-protected	create a new read transformer that refactor NDN cigar elements to one N element.	2014-04-28 11:29:00 -04:00
pom.xml	Update pom versions to mark the start of GATK 3.2 development	2014-03-18 01:18:59 -04:00