nicolas-bertin/CAGEscan-Clustering — pull request #3 by charles-plessy (2014-07-01 06:10:51+00:00)
Title: Add a note that read names ending by /1 /2 or /3 are consdered different by pairedBamToBed12.

Salut again,

we just got the problem that `foo/1` is not considered the same as `foo/3` by `pairedBamToBed12`. Here is a note to at least document the issue.

While the quickest way to solve the problem is to pre-process the BAM files, there must be a better solution. Do you think that it would be easy to let `pairedBamToBed12` the `\x` suffixes ?

Bon après-midi,

Charles