Fix option parsing

zwets · Jun 21, 2017 · f6cd15c · f6cd15c
1 parent da99203
commit f6cd15c
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Showing 15 changed files with 469 additions and 454 deletions.
diff --git a/uf b/uf
@@ -77,3 +77,4 @@ else
     END { print "\n" }' "$@"
 fi
 
+# vim: sts=4:sw=4:et:si:ai
diff --git a/uf-bare b/uf-bare
@@ -20,13 +20,13 @@
 
 # Function to exit this script with an error message on stderr
 err_exit() {
-	echo "$(basename "$0"): $*" >&2
-	exit 1
+    echo "$(basename "$0"): $*" >&2
+    exit 1
 }
 
 # Function to show usage information and exit
 usage_exit() {
-	echo "
+    echo "
 Usage: $(basename $0) [OPTIONS] [FILE ...]
 
   Output only the bare sequences from each FILE to standard output, dropping the
@@ -39,29 +39,29 @@ Usage: $(basename $0) [OPTIONS] [FILE ...]
   By default headers go to /dev/null.  Use option -w to store them in a file.
   The file can be merged back in with bare sequences using 'uf-dress'.
 " >&2
-	exit ${1:-1}
+    exit ${1:-1}
 }
 
 # Parse options
 
 unset HDRSFILE FORCE
 
 while [ $# -ne 0 -a "$(expr "$1" : '\(.\)..*')" = "-" ]; do
-	case $1 in
-	-w)	shift
-		[ $# -ge 1 ] || usage_exit
-		HDRSFILE="$1"
-		;;
-	-f|--force)
-		FORCE="yes"
-		;;
-	--help)
-		usage_exit 0
-		;;
-	*) usage_exit
-		;;
-	esac
-	shift
+    case $1 in
+    -w)    shift
+        [ $# -ge 1 ] || usage_exit
+        HDRSFILE="$1"
+        ;;
+    -f|--force)
+        FORCE="yes"
+        ;;
+    --help)
+        usage_exit 0
+        ;;
+    *) usage_exit
+        ;;
+    esac
+    shift
 done
 
 # Check options validity
@@ -71,6 +71,7 @@ done
 # Do the work
 
 awk -b -O -v F="$HDRSFILE" '
-	NR%2==1 && F { print > F }
-	NR%2==0' "$@"
+    NR%2==1 && F { print > F }
+    NR%2==0' "$@"
 
+# vim: sts=4:sw=4:et:si:ai
diff --git a/uf-circut b/uf-circut
@@ -20,13 +20,13 @@
 
 # Function to exit this script with an error message on stderr
 err_exit() {
-	echo "$(basename "$0"): $*" >&2
-	exit 1
+    echo "$(basename "$0"): $*" >&2
+    exit 1
 }
 
 # Function to show usage information and exit
 usage_exit() {
-	echo "
+    echo "
 Usage: $(basename $0) [OPTIONS] FROM:END [FILE ...]
        $(basename $0) [OPTIONS] FROM/LEN [FILE ...]
        $(basename $0) [OPTIONS] MID~DIST [FILE ...]
@@ -72,7 +72,7 @@ Usage: $(basename $0) [OPTIONS] FROM:END [FILE ...]
   - $(basename "$0") -10/21  Same result as above
   - $(basename "$0") 100:99  rotates the sequence left by 99 positions
 " >&2
-	exit ${1:-1}
+    exit ${1:-1}
 }
 
 # Parse options
@@ -81,24 +81,24 @@ QUIET=0
 ZERO=0
 MARK=0
 
-while [ $# -ne 0 -a "$(expr "$1" : '\(.[0-9]*\)..*')" = "-" ]; do
-	case $1 in
-	-m|--mark)
-		MARK=1
-		;;
-	-z|--zero)
-		ZERO=1
-		;;
-	-q|--quiet)
-		QUIET=1
-		;;
-	-h|--help)
-		usage_exit 0
-		;;
-	*) usage_exit
-		;;
-	esac
-	shift
+while [ $# -ne 0 -a "$(expr "$1" : '\(.\)..*')" = "-" ]; do
+    case $1 in
+    -m|--mark)
+        MARK=1
+        ;;
+    -z|--zero)
+        ZERO=1
+        ;;
+    -q|--quiet)
+        QUIET=1
+        ;;
+    -h|--help)
+        usage_exit 0
+        ;;
+    *) usage_exit
+        ;;
+    esac
+    shift
 done
 
 # Parse the cut specification - arrr walk the regex plank matey
@@ -117,7 +117,7 @@ RHS="$(expr "$CUT_SPEC" : '.*[/:~]\(.*\)')"
 # Delegate to awk
 
 awk -b -O -v P="$(basename "$0")" -v FROM=$LHS -v MID=$LHS -v UPTO=$RHS -v LEN=$RHS -v DIST=$RHS -v OP="$OP" -v Z=$ZERO -v Q=$QUIET -v M=$MARK '
-function bump0(p1,p2) { return p1 < 0 && p2 >= 0 ? 1 : 0 }	# return 1 if from p1 to p2 crosses 0
+function bump0(p1,p2) { return p1 < 0 && p2 >= 0 ? 1 : 0 }    # return 1 if from p1 to p2 crosses 0
 
 BEGIN { 
     # Translate the three possible cut specs into POS0 (left) and POS1 (right)
@@ -179,3 +179,4 @@ function validate() {
 }
 ' "$@"
 
+# vim: sts=4:sw=4:et:si:ai
diff --git a/uf-cut b/uf-cut
@@ -20,13 +20,13 @@
 
 # Function to exit this script with an error message on stderr
 err_exit() {
-	echo "$(basename "$0"): $*" >&2
-	exit 1
+    echo "$(basename "$0"): $*" >&2
+    exit 1
 }
 
 # Function to show usage information and exit
 usage_exit() {
-	echo "
+    echo "
 Usage: $(basename $0) [OPTIONS] FROM:END [FILE ...]
        $(basename $0) [OPTIONS] FROM/LEN [FILE ...]
        $(basename $0) [OPTIONS] MID~DIST [FILE ...]
@@ -69,7 +69,7 @@ Usage: $(basename $0) [OPTIONS] FROM:END [FILE ...]
   - '$(basename "$0") x/1'        Same result as previous
   - '$(basename "$0") x~0'        Same result as previous
 " >&2
-	exit ${1:-1}
+    exit ${1:-1}
 }
 
 # Parse options
@@ -79,27 +79,27 @@ ZERO=0
 CLIP=0
 MARK=0
 
-while [ $# -ne 0 -a "$(expr "$1" : '\(.[0-9]*\)..*')" = "-" ]; do
-	case $1 in
-	-m|--mark)
-		MARK=1
-		;;
-	-c|--clip)
-		CLIP=1
-		;;
-	-q|--quiet)
-		QUIET=1
-		;;
-	-z|--zero)
-		ZERO=1
-		;;
-	-h|--help)
-		usage_exit 0
-		;;
-	*) usage_exit
-		;;
-	esac
-	shift
+while [ $# -ne 0 -a "$(expr "$1" : '\(.\)..*')" = "-" ]; do
+    case $1 in
+    -m|--mark)
+        MARK=1
+        ;;
+    -c|--clip)
+        CLIP=1
+        ;;
+    -q|--quiet)
+        QUIET=1
+        ;;
+    -z|--zero)
+        ZERO=1
+        ;;
+    -h|--help)
+        usage_exit 0
+        ;;
+    *) usage_exit
+        ;;
+    esac
+    shift
 done
 
 # Parse the cut specification - arrr walk the regex plank matey
@@ -200,3 +200,4 @@ function validate_and_map() {
 }
 ' "$@"
 
+# vim: sts=4:sw=4:et:si:ai
diff --git a/uf-dress b/uf-dress
@@ -20,13 +20,13 @@
 
 # Function to exit this script with an error message on stderr
 err_exit() {
-	echo "$(basename "$0"): $*" >&2
-	exit 1
+    echo "$(basename "$0"): $*" >&2
+    exit 1
 }
 
 # Function to show usage information and exit
 usage_exit() {
-	echo "
+    echo "
 Usage: $(basename $0) [OPTIONS] [FILE ...]
 
   Insert headers to turn bare sequences into valid unfasta.  Reads each line from
@@ -45,26 +45,26 @@ Usage: $(basename $0) [OPTIONS] [FILE ...]
 
   See also: 'uf-map' which implements this idiom in a single command.
 " >&2
-	exit ${1:-1}
+    exit ${1:-1}
 }
 
 # Parse options
 
 unset HDRSFILE
 
 while [ $# -ne 0 -a "$(expr "$1" : '\(.\)..*')" = "-" ]; do
-	case $1 in
-	-r)	shift
-		[ $# -ge 1 ] || usage_exit
-		HDRSFILE="$1"
-		;;
-	--help)
-		usage_exit 0
-		;;
-	*) usage_exit
-		;;
-	esac
-	shift
+    case $1 in
+    -r)    shift
+        [ $# -ge 1 ] || usage_exit
+        HDRSFILE="$1"
+        ;;
+    --help)
+        usage_exit 0
+        ;;
+    *) usage_exit
+        ;;
+    esac
+    shift
 done
 
 # Check options validity
@@ -74,11 +74,12 @@ done
 # Do the work
 
 awk -b -O -v F="$HDRSFILE" '{
-	HDR = ""
-	if (F) getline HDR < F
-	if (!HDR) HDR = ">lcl|" NR " Dummy header " NR
-	print HDR
-	print
-	} 
-	END { if (F) close (F) }' "$@"
+    HDR = ""
+    if (F) getline HDR < F
+    if (!HDR) HDR = ">lcl|" NR " Dummy header " NR
+    print HDR
+    print
+    } 
+    END { if (F) close (F) }' "$@"
 
+# vim: sts=4:sw=4:et:si:ai
diff --git a/uf-drop b/uf-drop
@@ -20,13 +20,13 @@
 
 # Function to exit this script with an error message on stderr
 err_exit() {
-	echo "$(basename "$0"): $*" >&2
-	exit 1
+    echo "$(basename "$0"): $*" >&2
+    exit 1
 }
 
 # Function to show usage information and exit
 usage_exit() {
-	echo "
+    echo "
 Usage: $(basename $0) [OPTIONS] NUM [FILE ...]
 
   For each sequence in each unfasta format FILE drop the first NUM characters
@@ -38,7 +38,7 @@ Usage: $(basename $0) [OPTIONS] NUM [FILE ...]
    -b|--but   Drop everything BUT the final NUM characters from each sequence.
    -m|--mark  Document the edit by appending '(uf:drop:[but:]NUM)' to headers.
 " >&2
-	exit ${1:-1}
+    exit ${1:-1}
 }
 
 # Parse options
@@ -47,20 +47,20 @@ BUT=0
 MARK=0
 
 while [ $# -ne 0 -a "$(expr "$1" : '\(.\)..*')" = "-" ]; do
-	case $1 in
-	-m|--mark)
-		MARK=1
-		;;
-	-b|--but)
-		BUT=1
-		;;
-	-h|--help)
-		usage_exit 0
-		;;
-	*) usage_exit
-		;;
-	esac
-	shift
+    case $1 in
+    -m|--mark)
+        MARK=1
+        ;;
+    -b|--but)
+        BUT=1
+        ;;
+    -h|--help)
+        usage_exit 0
+        ;;
+    *) usage_exit
+        ;;
+    esac
+    shift
 done
 
 # Check first argument is positive number
@@ -73,7 +73,8 @@ shift
 # Delegate to awk
 
 awk -b -O -v P="$(basename "$0")" -v N=$NUM -v M=$MARK -v B=$BUT '
-	NR%2==1 { print $0 (M ? " (uf:drop:" (B?"but:":"") N ")" : "") }
-	NR%2==0 { print B ? substr ($0,length($0)-N+1) : substr ($0,N+1) }
-	' "$@"
+    NR%2==1 { print $0 (M ? " (uf:drop:" (B?"but:":"") N ")" : "") }
+    NR%2==0 { print B ? substr ($0,length($0)-N+1) : substr ($0,N+1) }
+    ' "$@"
 
+# vim: sts=4:sw=4:et:si:ai
Original file line number	Diff line number	Diff line change
Expand Up		@@ -77,3 +77,4 @@ else
		END { print "\n" }' "$@"
		fi

		# vim: sts=4:sw=4:et:si:ai