NAME

       fastahack  -  fastahack  -  indexing  and extracting sequences and subsequences from FASTA
       files

DESCRIPTION

       usage: fastahack [options] <fasta reference>

   options:
       -i, --index
              generate fasta index <fasta reference>.fai

       -r, --region REGION
              print the specified region

       -c, --stdin
              read  a  stream  of  line-delimited  region  specifiers  on  stdin  and  print  the
              corresponding sequence for each on stdout

       -e, --entropy
              print the shannon entropy of the specified region

       -d, --dump
              print the fasta file in the form 'seq_name <tab> sequence'

       REGION  is  of  the  form  <seq>, <seq>:<start>[sep]<end>, <seq1>:<start>[sep]<seq2>:<end>
       where start and end are 1-based, and the region includes the end position.  [sep]  is  "-"
       or ".."

       Specifying  a  sequence  name alone will return the entire sequence, specifying range will
       return that range, and specifying a  single  coordinate  pair,  e.g.   <seq>:<start>  will
       return just that base.

       author: Erik Garrison <erik.garrison@bc.edu>