#! /bin/bash 
# Last edited on 2015-10-31 01:10:56 by stolfilocal

seqA="$1"; shift;      # Tag (short name) of sequence A. 
seqB="$1"; shift;      # Tag (short name) of sequence B. 
tool="$1"; shift;      # Tool used to create the LAV file ("FASTA", "LASTZ", etc.)
minRungs="$1"; shift;  # Min number of rungs per candidate.
minGood="$1"; shift;   # Two-digit percentage 00 to 99 only.

# Assumes that the LAV file was created with LASTZ.

infile="cdv/${seqA}_${seqB}_${tool}_${minRungs}_${minGood}.cdv"
outfile="cdv/${seqA}_${seqB}_${tool}_${minRungs}_FF.cdv"

dm_scramble_cands \
  -verbose \
  < ${infile} \
  > ${outfile}