4. Script

This is a script which you can use to call SJC clean:

#! /bin/bash
# clean Raw Data Files
# calls "SJBclean"
# input: files are in b2zip-format
# output: ./$PREFIX/*.$PREFIX
#

MODE=FRQ
TEMPFILE=/tmp/SJBclean
PREFIX=pre

mkdir ./$PREFIX

for FILE in *.frq.*.bz2
do
  echo SJBclean $FILE $MODE $TEMPFILE
  bunzip2 -k -c $FILE | sjbclean $MODE $TEMPFILE | bzip2 >./$PREFIX/$FILE.$PREFIX
done