taoliu/MACS — pull request #39 by JohnUrban (2014-06-04 19:00:51+00:00)
Title: calmaxtag subcommand

Hi Tao,

If you are interested, I added a new subcommand called "calmaxtag" which is essentially a stripped down version of 'filterdup' that tells the user how many tags would be be allowed per site if they chose to use the 'auto' option. For example, "macs2 calmaxtag -g genome_size [-n numTags | -i inputFile]" calculates the maximum number of duplicate tags to leave at a site based on "-g genome_size" and either "-n numTags" or "-i inputFile". It is a simple addition to the set of macs2 subcommands that gives direct access to the MACS2 calculation without any other strings attached, especially if the number of tags is known in advance (-n option). It has been useful to me when exploring which macs2 settings I would like to use with a new data set and for 'on the fly' calculations for how many tags MACS2 would leave with the 'auto' option when talking to my advisor and/or collaborators. I have had this for a while and thought others might also find it useful to have.

best,
John Urban

p.s. I should note that I did not knowingly delete the "options.ratio" -- if I did that was accidental and they should be restored.