#!/bin/csh -f

# Copyright @ 2000 The Institute for Genomic Research (TIGR). All rights
# reserved.
#
# This software is provided "AS IS". The Institute for Genomic Research makes
# no warranties, express or implied, including no representation or warranty
# with respect to the performance of the software and derivatives or their
# safety, effectiveness, or commercial viability. TIGR does not warrant the
# merchantability or fitness of the software and derivatives for any
# particular purpose, or that they may be exploited without infringing the
# copyrights, patent rights or property rights of others.
#
# This software program may not be sold, leased, transferred, exported or
# otherwise disclosed to anyone, in whole or in part, without written consent
# of TIGR.

unset noclobber
if (! -e "${1}") then
	set asmg_options="${1}"
	shift
else
	set asmg_options=""
endif
foreach file (${argv[*]})
	set file_tail=${file:t}
	set file_root=${file_tail:r}
	(TIGR_Assembler -n ${file_root} -g 8 -l 40 -e 15 -p 97.5 -a ${file_root}.align -f ${file_root}.fasta ${asmg_options} ${file_root}.scratch < ${file} >! ${file_root}.asm) >&! ${file_root}.error
end