petercombs/EisenLab-Code — pull request #1 by petercombs (2012-05-11 23:20:26+00:00)
Title: General changes to do_tux

* Remove call to samtools rmdup
rmdup is overconservative in removing "duplicates". I have a better way of estimating this.
* Add call to samtools index
I thought this might be useful, and in any case is quick and takes up relatively little space.
* Fix reference to "analysis"
Should point to the variable analysis_dir in the call to cuffdiff