Fix handling of dash as file name

uf-bare

@@ -46,7 +46,7 @@ Usage: $(basename $0) [OPTIONS] [FILE] ...
 
 unset HDRSFILE FORCE
 
-while [ $# -ne 0 -a "$(expr "$1" : '\(.\).*')" = "-" ]; do
+while [ $# -ne 0 -a "$(expr "$1" : '\(.\)..*')" = "-" ]; do
 	case $1 in
 	-w)	shift
 		[ $# -ge 1 ] || usage_exit

uf-dress

@@ -52,7 +52,7 @@ Usage: $(basename $0) [OPTIONS] [FILE] ...
 
 unset HDRSFILE
 
-while [ $# -ne 0 -a "$(expr "$1" : '\(.\).*')" = "-" ]; do
+while [ $# -ne 0 -a "$(expr "$1" : '\(.\)..*')" = "-" ]; do
 	case $1 in
 	-r)	shift
 		[ $# -ge 1 ] || usage_exit

uf-freqs

@@ -47,7 +47,7 @@ BARE=0
 LENGTH_ONLY=0
 TOTALS=0
 
-while [ $# -ne 0 -a "$(expr "$1" : '\(.[0-9]*\).*')" = "-" ]; do
+while [ $# -ne 0 -a "$(expr "$1" : '\(.[0-9]*\)..*')" = "-" ]; do
 	case $1 in
 	-b|--bare)
 		BARE=1

uf-headers

@@ -37,7 +37,7 @@ Usage: $(basename $0) [OPTIONS] [FILE] ...
 
 # Parse options
 
-while [ $# -ne 0 -a "$(expr "$1" : '\(.\).*')" = "-" ]; do
+while [ $# -ne 0 -a "$(expr "$1" : '\(.\)..*')" = "-" ]; do
 	case $1 in
 	--help)
 		usage_exit 0

uf-rc

@@ -38,7 +38,7 @@ err_exit() {
 # Function to show usage information and exit
 usage_exit() {
 	echo "
-Usage: $(basename $0) [OPTIONS] [FILE] ...
+Usage: $(basename $0) [OPTIONS] [FILE ...]
 
   Write to standard output the reverse complement of every sequence in each FILE.
   If no FILE is present or FILE is '-', read from standard input.
@@ -62,7 +62,7 @@ MARK=0
 
 # Parse options
 
-while [ $# -ne 0 -a "$(expr "$1" : '\(.\).*')" = "-" ]; do
+while [ $# -ne 0 -a "$(expr "$1" : '\(.\)..*')" = "-" ]; do
 	case $1 in
 	-r|--reverse-only)
 		COMPLEMENT=0

uf-select

@@ -27,7 +27,7 @@ err_exit() {
 # Function to show usage information and exit
 usage_exit() {
 	echo "
-Usage: $(basename $0) [OPTIONS|NUMBERS|REGEX] [FILE] ...
+Usage: $(basename $0) [OPTIONS|NUMBERS|REGEX] [FILE ...]
 
   Select sequences from unfasta FILEs and write to standard output.  If no FILE
   is present or when FILE is '-', read standard input.
@@ -66,6 +66,9 @@ while [ $# -ne 0 -a "$(expr "$1" : '\(.[0-9]*\).*')" = "-" ]; do
 	-h|--help)
 		usage_exit 0
 		;;
+	-)
+		break
+		;;
 	*) usage_exit
 		;;
 	esac

uf-valid

@@ -58,7 +58,7 @@ err_exit() {
 # Function to show usage information and exit
 usage_exit() {
 	echo "
-Usage: $(basename $0) [OPTIONS] [FILE] ...
+Usage: $(basename $0) [OPTIONS] [FILE ...]
 
   Validate the sequences in each FILE against the allowed alphabet.  If no FILE
   is present or FILE is '-', read from standard input.  Only valid sequences are
@@ -98,7 +98,7 @@ QUIET=0
 
 # Parse options
 
-while [ $# -ne 0 -a "$(expr "$1" : '\(.\).*')" = "-" ]; do
+while [ $# -ne 0 -a "$(expr "$1" : '\(.\)..*')" = "-" ]; do
 	case $1 in
 	--allow=*)
 		ALLOW="${ALLOW}${1#"--allow="}"