moved up LC command so sort is correct

#             match any files with the read1str.   

#set -e ## This is causing problems; need better error detection

shopt -s extglob

export LC_ALL=C

juicer_version="1.5.6" 

### LOAD BWA AND SAMTOOLS

            echo "(-: $name$ext.sam created successfully."

	fi

	export LC_ALL=C

        # call chimeric_blacklist.awk to deal with chimeric reads; 

        # sorted file is sorted by read name at this point

	touch $name${ext}_abnorm.sam $name${ext}_unmapped.sam