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barricklab / breseq

breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA resequencing data. It is intended for haploid microbial genomes (<20 Mb). breseq is a command line tool implemented in C++ and R.
http://barricklab.org/breseq
GNU General Public License v2.0
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samtools included with patch #367

Closed alexmyczko closed 2 months ago

alexmyczko commented 7 months ago

what is the exact reason and details on this patch?

http://sid.ethz.ch/debian/breseq/2024/breseq-0.38.3/extern/samtools_modifications.txt

asking for this: https://github.com/barricklab/breseq/issues/181

jeffreybarrick commented 7 months ago

It's been a long time since I looked at this...

Conceptually, these changes were made so breseq can build and link to its own private and stable version of samtools that has a modification such that it will return all alignments of a read and not just the first 8000.

So, if this question is related to making a breseq package, one thing to know is that you should not list samtools as a separate prerequisite.