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Old 02-11-2014, 09:43 AM   #14
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

It's very close to the code in bowtie2. This is from bison (a BS-seq aligner I wrote that uses bowtie2 as the underlying aligner), which is written in C, rather than bowtie2, which is written in C++, but aside from the language/interface difference most of the code will be identical (there aren't that many ways to code that algorithm, frankly).

Edit: I believe the bowtie2 function is in unique.h, if you're curious (there are 3 versions there, #2 seems to be the one used, at least up to version 2.1.0).

Last edited by dpryan; 02-11-2014 at 09:45 AM.
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