PrimerCut is a tool for differentially cutting the primer sequence in
aligned reads depending on where the primer sequence derived from (genomic DNA
or PCR primers).

REQUIREMENTS
------------

To use PrimerCut you need
  * ruby 1.9
  * ruby gems:
     * bio
     * bio-samtools

USING
-----

Usage: PrimerCut [regions]
    -i, --input FILE                             Input BAM
    -o, --output FILE                            Output BAM
    -r, --regions [a,b,c or regions.bed]         Regions to remove

E.g.:
    PrimerCut -i source.bam -o target.bam -r 1:1070-1100,4:4500-4530
    PrimerCut -i source.bam -o target.bam -r regions.bed


LINKS
-----
ftp://rogaevlab.ru/PrimerCut
http://github.com/gusevfe/primercut