#!/bin/sh

# For each name in INFILE, call a SeqHound method, and return
# the result (a list). Results for each name are converted into
# a GDE flat file. Flat files are concatenated into a single
# flatfile to be read back into GDE.

# Make sure that the user has a $HOME/.shoundremrc file
if [ ! -f $HOME/.shoundremrc ] 
   then
   ln -s $BIRCH/java/Leash/shoundremrc $HOME/.shoundremrc
fi


# RM_CMD - command to be used for removing files and directories
if [ -f /usr/bin/rm ] 
   then
     RM_CMD=/usr/bin/rm
   else
     if [ -f /bin/rm ] 
        then
           RM_CMD=/bin/rm
        else
           RM_CMD=rm
     fi
fi
 

INFILE=$1
shift
OUTFILE=$1
shift
TYPE=$1
shift

cat $INFILE |
while read name
  do
    echo $name
    java -jar $birch/java/Leash/Leash.jar -mpi $name $* -of $name.$TYPE
    python $BIRCH/script/list2flat.py $name.$TYPE leash.$$
    cat leash.$$ >> $OUTFILE
    $RM_CMD $name.$TYPE leash.$$
  done