diff --git a/uf b/uf
index 4d59455..cf7e632 100755
--- 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
index e424ede..ecc639b 100755
--- 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
@@ -39,7 +39,7 @@ 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
@@ -47,21 +47,21 @@ Usage: $(basename $0) [OPTIONS] [FILE ...]
 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
index 5a9e3d2..e4704c6 100755
--- 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
index 0477bb3..fad5aa7 100755
--- 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
index 39999e3..ac850f0 100755
--- 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
@@ -45,7 +45,7 @@ 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
@@ -53,18 +53,18 @@ Usage: $(basename $0) [OPTIONS] [FILE ...]
 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
index 5e49d8b..15427f2 100755
--- 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
diff --git a/uf-freqs b/uf-freqs
index 7914f04..0039392 100755
--- a/uf-freqs
+++ b/uf-freqs
@@ -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 ...]
 
   Count frequencies of elements in each sequence in each unfasta FILE and write
@@ -38,7 +38,7 @@ Usage: $(basename $0) [OPTIONS] [FILE ...]
    -l|--length-only   Length of sequence only, no frequencies per element
    -t|--totals        Totals across all sequences at bottom
 " >&2
-	exit ${1:-1}
+    exit ${1:-1}
 }
 
 # Parse options
@@ -47,46 +47,47 @@ BARE=0
 LENGTH_ONLY=0
 TOTALS=0
 
-while [ $# -ne 0 -a "$(expr "$1" : '\(.[0-9]*\)..*')" = "-" ]; do
-	case $1 in
-	-b|--bare)
-		BARE=1
-		;;
-	-l|--length*)
-		LENGTH_ONLY=1
-		;;
-	-t|--totals)
-		TOTALS=1
-		;;
-	-h|--help)
-		usage_exit 0
-		;;
-	*) usage_exit
-		;;
-	esac
-	shift
+while [ $# -ne 0 -a "$(expr "$1" : '\(.\)..*')" = "-" ]; do
+    case $1 in
+    -b|--bare)
+        BARE=1
+        ;;
+    -l|--length*)
+        LENGTH_ONLY=1
+        ;;
+    -t|--totals)
+        TOTALS=1
+        ;;
+    -h|--help)
+        usage_exit 0
+        ;;
+    *) usage_exit
+        ;;
+    esac
+    shift
 done
 
 awk -b -O -v P="$(basename "$0")" -v BARE=$BARE -v LENGTH_ONLY=$LENGTH_ONLY -v TOTALS=$TOTALS '
 BEGIN { PROCINFO["sorted_in"] = "@ind_str_asc" }
 NR%2==1 && !BARE 
 NR%2==0 {
-	for (i=1; i<=length($0); ++i) freqs[toupper(substr($0,i,1))] += 1
-	printf length($0)
-	if (!LENGTH_ONLY) for (j in freqs) printf " " j "=" freqs[j]
-	printf "\n"
-	if (TOTALS) {
-		for (j in freqs) totals[j] += freqs[j]
-		grand_total += length($0)
-	}
+    for (i=1; i<=length($0); ++i) freqs[toupper(substr($0,i,1))] += 1
+    printf length($0)
+    if (!LENGTH_ONLY) for (j in freqs) printf " " j "=" freqs[j]
+    printf "\n"
+    if (TOTALS) {
+        for (j in freqs) totals[j] += freqs[j]
+        grand_total += length($0)
+    }
 }
 END { 
-	if (TOTALS) {
-		if (!BARE) print ">TOTALS"
-		printf grand_total;
-		if (!LENGTH_ONLY) for (j in totals) printf " " j "=" totals[j]
-		printf "\n"
-	}
+    if (TOTALS) {
+        if (!BARE) print ">TOTALS"
+        printf grand_total;
+        if (!LENGTH_ONLY) for (j in totals) printf " " j "=" totals[j]
+        printf "\n"
+    }
 } 
 ' "$@"
 
+# vim: sts=4:sw=4:et:si:ai
diff --git a/uf-hash b/uf-hash
index 6d5507d..f5ff89f 100755
--- a/uf-hash
+++ b/uf-hash
@@ -23,13 +23,13 @@ ALGO="md5"
 
 # 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 ...]
 
   Computes a hash over the sequence content of unfasta FILEs, or stdin if
@@ -42,28 +42,28 @@ Usage: $(basename $0) [OPTIONS] [FILE ...]
   OPTIONS
    -a|--algo ALG     Use algorithm md5/sha1/224/256/384/512, default: $ALGO
 " >&2
-	exit ${1:-1}
+    exit ${1:-1}
 }
 
 # Parse options
 
 unset REORDERABLE
-while [ $# -ne 0 -a "$(expr "$1" : '\(.[0-9]*\)..*')" = "-" ]; do
-	case $1 in
-	--algo=*)
-		ALGO=${1#--algo=}
-		;;
-	-a|--algo*)
-		shift
-		ALGO=$1
-		;;
-	-h|--help)
-		usage_exit 0
-		;;
-	*) usage_exit
-		;;
-	esac
-	shift
+while [ $# -ne 0 -a "$(expr "$1" : '\(.\)..*')" = "-" ]; do
+    case $1 in
+    --algo=*)
+        ALGO=${1#--algo=}
+        ;;
+    -a|--algo*)
+        shift
+        ALGO=$1
+        ;;
+    -h|--help)
+        usage_exit 0
+        ;;
+    *) usage_exit
+        ;;
+    esac
+    shift
 done
 
 # Check options and arguments
@@ -80,3 +80,4 @@ FILE="-"
 
 awk -b -O 'NR % 2 == 0' "$FILE" | $HASH_PGM | cut -d' ' -f1
 
+# vim: sts=4:sw=4:et:si:ai
diff --git a/uf-headers b/uf-headers
index 76935c4..2806072 100755
--- a/uf-headers
+++ b/uf-headers
@@ -20,33 +20,34 @@
 
 # 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 ...]
 
   Drop the sequence data and output only the headers from each FILE.
   If no FILE is present or FILE is '-', read from standard input.
 " >&2
-	exit ${1:-1}
+    exit ${1:-1}
 }
 
 # Parse options
 
 while [ $# -ne 0 -a "$(expr "$1" : '\(.\)..*')" = "-" ]; do
-	case $1 in
-	--help)
-		usage_exit 0
-		;;
-	*) usage_exit
-		;;
-	esac
-	shift
+    case $1 in
+    --help)
+        usage_exit 0
+        ;;
+    *) usage_exit
+        ;;
+    esac
+    shift
 done
 
 awk -b -O 'NR%2==1' "$@"
 
+# vim: sts=4:sw=4:et:si:ai
diff --git a/uf-random b/uf-random
index b55cba6..3e0b473 100755
--- a/uf-random
+++ b/uf-random
@@ -24,13 +24,13 @@ SEQ_LENGTH=100
 
 # 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] [CHARS]
 
   Write to standard output an unfasta file with randomly generated sequences.
@@ -49,48 +49,48 @@ Usage: $(basename $0) [OPTIONS] [CHARS]
   NOTE: the current implementation uses the \$RANDOM builtin to obtain random
   numbers. This is bash specific. TODO: change to read from /dev/urandom.
 " >&2
-	exit ${1:-1}
+    exit ${1:-1}
 }
 
 # Parse options
 
-while [ $# -ne 0 -a "$(expr "$1" : '\(.\).*')" = "-" ]; do
-	case $1 in
-	--count=*)
-                SEQ_COUNT=${1#--count=}
-                ;;
-        -c|--count)
-                shift
-                SEQ_COUNT=$1
-                ;;
-	--length=*)
-                SEQ_LENGTH=${1#--length=}
-                ;;
-        -l|--length)
-                shift
-                SEQ_LENGTH=$1
-                ;;
-	--range=*)
-                RANGE=${1#--range=}
-                ;;
-        -r|--range)
-                shift
-                RANGE=$1
-                ;;
-	--help)
-		usage_exit 0
-		;;
-	*) usage_exit
-		;;
-	esac
-	shift
+while [ $# -ne 0 -a "$(expr "$1" : '\(.\)..*')" = "-" ]; do
+    case $1 in
+    --count=*)
+        SEQ_COUNT=${1#--count=}
+        ;;
+    -c|--count)
+        shift
+        SEQ_COUNT=$1
+        ;;
+    --length=*)
+        SEQ_LENGTH=${1#--length=}
+        ;;
+    -l|--length)
+        shift
+        SEQ_LENGTH=$1
+        ;;
+    --range=*)
+        RANGE=${1#--range=}
+        ;;
+    -r|--range)
+        shift
+        RANGE=$1
+        ;;
+    --help)
+        usage_exit 0
+        ;;
+    *) usage_exit
+        ;;
+    esac
+    shift
 done
 
 # Parse arguments
 
 if [ $# -eq 1 ]; then
-	SEQ_CHARS="$1"
-	shift
+    SEQ_CHARS="$1"
+    shift
 fi
 
 [ $# -eq 0 ] || usage_exit
@@ -98,10 +98,10 @@ fi
 # Parse MIN and MAX if random lengths are required
 
 if [ -n "$RANGE" ]; then
-	MIN_LENGTH="$(expr "$RANGE" : '\([0-9]\+\),[0-9]\+$')" || err_exit "not a valid range specification: $RANGE"
-	MAX_LENGTH="$(expr "$RANGE" : '[0-9]\+,\([0-9]\+\)$')" || err_exit "not a valid range specification: $RANGE"
-	RANGE_SIZE=$((MAX_LENGTH - MIN_LENGTH + 1))
-	[ $RANGE_SIZE -gt 0 ] || err_exit "invalid range: $RANGE"
+    MIN_LENGTH="$(expr "$RANGE" : '\([0-9]\+\),[0-9]\+$')" || err_exit "not a valid range specification: $RANGE"
+    MAX_LENGTH="$(expr "$RANGE" : '[0-9]\+,\([0-9]\+\)$')" || err_exit "not a valid range specification: $RANGE"
+    RANGE_SIZE=$((MAX_LENGTH - MIN_LENGTH + 1))
+    [ $RANGE_SIZE -gt 0 ] || err_exit "invalid range: $RANGE"
 fi
 
 # Check that we have RANDOM, which is a bash extension - @TODO migrate to /dev/urandom
@@ -111,11 +111,12 @@ expr "$RANDOM" : '[0-9]\+$' >/dev/null || err_exit "\$RANDOM not supported by sh
 # Generate the sequences 
 
 for (( S = 1 ; S <= $SEQ_COUNT ; S += 1 )); do
-	[ -z "$RANGE" ] || SEQ_LENGTH=$((MIN_LENGTH + ($RANDOM % RANGE_SIZE)))
-	echo ">lcl|$S Random sequence $S (length $SEQ_LENGTH)"
-	for (( C = 1 ; C <= SEQ_LENGTH ; C += 1 )); do
-		echo -n ${SEQ_CHARS:$(($RANDOM % ${#SEQ_CHARS})):1}
-	done
-	echo
+    [ -z "$RANGE" ] || SEQ_LENGTH=$((MIN_LENGTH + ($RANDOM % RANGE_SIZE)))
+    echo ">lcl|$S Random sequence $S (length $SEQ_LENGTH)"
+    for (( C = 1 ; C <= SEQ_LENGTH ; C += 1 )); do
+        echo -n ${SEQ_CHARS:$(($RANDOM % ${#SEQ_CHARS})):1}
+    done
+    echo
 done
 
+# vim: sts=4:sw=4:et:si:ai
diff --git a/uf-rc b/uf-rc
index 20b8a9e..a2782ae 100755
--- a/uf-rc
+++ b/uf-rc
@@ -31,27 +31,27 @@ COMP_ALPHABET="TtGgCcAaNnMmKkWwSsRrYyVvBbHhDd"
 
 # 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 ...]
 
   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.
 
-  Options
-   -r|--reverse-only     Reverse only, do not complement.
-   -c|--complement-only  Complement only, do not reverse.
-   -m|--mark[-header]    Document operation by attaching '(uf:...)' to headers.
+  OPTIONS
+   -r, --reverse-only     Reverse only, do not complement.
+   -c, --complement-only  Complement only, do not reverse.
+   -m, --mark[-header]    Document operation by attaching '(uf:...)' to headers.
 
   Case is preserved.  Will also work for the degenerate nucleotide letters.
   E.g. complement of Y (pyrimidine, T/C) is R (purine, A/T).
 " >&2
-	exit ${1:-1}
+    exit ${1:-1}
 }
 
 # Defaults
@@ -63,44 +63,45 @@ MARK=0
 # Parse options
 
 while [ $# -ne 0 -a "$(expr "$1" : '\(.\)..*')" = "-" ]; do
-	case $1 in
-	-r|--reverse-only)
-		COMPLEMENT=0
-		;;
-	-c|--complement-only)
-		REVERSE=0
-		;;
-	-m|--mark*)
-		MARK=1
-		;;
-	--help)
-		usage_exit 0
-		;;
-	*) usage_exit
-		;;
-	esac
-	shift
+    case $1 in
+    -r|--reverse-only)
+        COMPLEMENT=0
+        ;;
+    -c|--complement-only)
+        REVERSE=0
+        ;;
+    -m|--mark*)
+        MARK=1
+        ;;
+    --help)
+        usage_exit 0
+        ;;
+    *) usage_exit
+        ;;
+    esac
+    shift
 done
 
 # Do the work
 
 awk -b -O -v P="$(basename "$0")" -v C=$COMPLEMENT -v R=$REVERSE -v M=$MARK '
-	NR%2==1 { print $0 (M ? " (uf:" (R?"reverse":"") (C?"complement":"") ")" : "") }
-	NR%2==0 {
-		if (R) for (i = length($0); i >= 1; --i) print_maybe_comp()
-		else   for (i = 1; i <= length($0); ++i) print_maybe_comp()
-		printf "\n"
-	}
-	function print_maybe_comp(     c,p) {	# Haha, globals rule, no need to pass i
-		c = substr ($0,i,1)
-		if (C) {
-			p = index ("'$NUCL_ALPHABET'", c)
-			if (!p) {
-				print P ": invalid character, cannot complement: " c
-				exit 1
-			}
-			c = substr ("'$COMP_ALPHABET'", p, 1)
-		}
-		printf "%c", c
-	}' "$@"
+    NR%2==1 { print $0 (M ? " (uf:" (R?"reverse":"") (C?"complement":"") ")" : "") }
+    NR%2==0 {
+        if (R) for (i = length($0); i >= 1; --i) print_maybe_comp()
+        else   for (i = 1; i <= length($0); ++i) print_maybe_comp()
+        printf "\n"
+    }
+    function print_maybe_comp(     c,p) {    # Haha, globals rule, no need to pass i
+        c = substr ($0,i,1)
+        if (C) {
+            p = index ("'$NUCL_ALPHABET'", c)
+            if (!p) {
+                print P ": invalid character, cannot complement: " c
+                exit 1
+            }
+            c = substr ("'$COMP_ALPHABET'", p, 1)
+        }
+        printf "%c", c
+    }' "$@"
 
+# vim: sts=4:sw=4:et:si:ai
diff --git a/uf-select b/uf-select
index cb34617..894e069 100755
--- a/uf-select
+++ b/uf-select
@@ -20,71 +20,71 @@
 
 # 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|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.
 
   OPTIONS
-   -n|--nth N[,..]  Select the nth sequence(s) for each file.
-   -g|--grep REGEX  Select the sequence(s) whose header matches REGEX.
+   -n, --nth N[,..]  Select the nth sequence(s) for each file.
+   -g, --grep REGEX  Select the sequence(s) whose header matches REGEX.
 
   As a convenience, when no option is specified then if the first argument 
   parses as a valid list of NUMBERS then --nth is assumed, else --grep is
   assumed.
 " >&2
-	exit ${1:-1}
+    exit ${1:-1}
 }
 
 # Parse options
 
 unset NTH REGEX
 
-while [ $# -ne 0 -a "$(expr "$1" : '\(.[0-9]*\)..*')" = "-" ]; do
-	case $1 in
-	--nth=*)
-		NTH=${1#--nth=}
-		;;
-	-n|--nth)
-		shift
-		NTH=$1
-		;;
-	--grep=*)
-		REGEX=${1#--grep=}
-		;;
-	-g|--grep)
-		shift
-		REGEX=$1
-		;;
-	-h|--help)
-		usage_exit 0
-		;;
-	-)
-		break
-		;;
-	*) usage_exit
-		;;
-	esac
-	shift
+while [ $# -ne 0 -a "$(expr "$1" : '\(.\)..*')" = "-" ]; do
+    case $1 in
+    --nth=*)
+        NTH=${1#--nth=}
+        ;;
+    -n|--nth)
+        shift
+        NTH=$1
+        ;;
+    --grep=*)
+        REGEX=${1#--grep=}
+        ;;
+    -g|--grep)
+        shift
+        REGEX=$1
+        ;;
+    -h|--help)
+        usage_exit 0
+        ;;
+    -)
+        break
+        ;;
+    *) usage_exit
+        ;;
+    esac
+    shift
 done
 
 # Handle option-less case
 
 if [ -z "$NTH" ] && [ -z "$GREP" ]; then
-	[ -n "$1" ] || usage_exit
-	if expr "$1" : '\([0-9]\+\(,[0-9]\+\)*$\)' >/dev/null; then
-		NTH="$1"
-	else
-		REGEX="$1"
-	fi
-	shift
+    [ -n "$1" ] || usage_exit
+    if expr "$1" : '\([0-9]\+\(,[0-9]\+\)*$\)' >/dev/null; then
+        NTH="$1"
+    else
+        REGEX="$1"
+    fi
+    shift
 fi
 
 # Check options
@@ -95,16 +95,17 @@ fi
 # Do the work
 
 if [ -n "$NTH" ]; then
-	#awk -b -O -v NTH=$NTH 'BEGIN { split(NTH,lines,/,/) } int((NR+1)/2) in lines' "$@"
-	awk -b -O -v NTH=$NTH '
-	BEGIN { split(NTH,lines,/,/) } 
-	{ for (x in lines) if (int((NR+1)/2) == lines[x]) print }
-	' "$@"
+    #awk -b -O -v NTH=$NTH 'BEGIN { split(NTH,lines,/,/) } int((NR+1)/2) in lines' "$@"
+    awk -b -O -v NTH=$NTH '
+    BEGIN { split(NTH,lines,/,/) } 
+    { for (x in lines) if (int((NR+1)/2) == lines[x]) print }
+    ' "$@"
 elif [ -n "$REGEX" ]; then
-	awk -b -O '
+    awk -b -O '
         NR % 2 == 1 && /'$REGEX'/ { print; getline; print }
-	' "$@"
+    ' "$@"
 else
-	usage_exit
+    usage_exit
 fi
 
+# vim: sts=4:sw=4:et:si:ai
diff --git a/uf-sort b/uf-sort
index a8fbf4c..d8dded7 100755
--- a/uf-sort
+++ b/uf-sort
@@ -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 ...]
 
   Sort the sequences in unfasta FILEs in order of decreasing length, and
@@ -36,25 +36,25 @@ Usage: $(basename $0) [OPTIONS] [FILE ...]
   OPTIONS
    -r|--reverse   Reverse the order of the sort
 " >&2
-	exit ${1:-1}
+    exit ${1:-1}
 }
 
 # Parse options
 
 unset REVERSE
 
-while [ $# -ne 0 -a "$(expr "$1" : '\(.[0-9]*\)..*')" = "-" ]; do
-	case $1 in
-	-r|--reverse)
-		REVERSE="-r"
-		;;
-	-h|--help)
-		usage_exit 0
-		;;
-	*) usage_exit
-		;;
-	esac
-	shift
+while [ $# -ne 0 -a "$(expr "$1" : '\(.\)..*')" = "-" ]; do
+    case $1 in
+    -r|--reverse)
+        REVERSE="-r"
+        ;;
+    -h|--help)
+        usage_exit 0
+        ;;
+    *) usage_exit
+        ;;
+    esac
+    shift
 done
 
 # Do the work
@@ -67,12 +67,13 @@ done
 
 # Pre-process into single records
 awk -b -O -v OFS='\t' '
-	NR % 2 == 1 { HDR = $0; }
-	NR % 2 == 0 { print length(), $0, HDR }
-	' "$@" |
+    NR % 2 == 1 { HDR = $0; }
+    NR % 2 == 0 { print length(), $0, HDR }
+    ' "$@" |
 # Sort in order
-#LC_ALL=C sort $REVERSE --buffer-size=1G --key='1rn,2' -t '	' - |
-LC_ALL=C sort $REVERSE --key='1rn,2' -t '	' - |
+#LC_ALL=C sort $REVERSE --buffer-size=1G --key='1rn,2' -t '    ' - |
+LC_ALL=C sort $REVERSE --key='1rn,2' -t '    ' - |
 # And unpack again - let's hope there are no tabs in headers ...
 awk -b -O -F '\t' '{ print $3; print $2; }'
 
+# vim: sts=4:sw=4:et:si:ai
diff --git a/uf-take b/uf-take
index 9e033f2..4762738 100755
--- a/uf-take
+++ b/uf-take
@@ -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 write the first NUM characters
@@ -34,10 +34,10 @@ Usage: $(basename $0) [OPTIONS] NUM [FILE ...]
   input.  With modifier -b|--but, take all except the final NUM characters.
 
   Options
-   -b|--but   Copy everything BUT the final NUM characters from each sequence.
-   -m|--mark  Document the edit by appending '(uf:take:[but:]NUM)' to headers.
+   -b, --but   Copy everything BUT the final NUM characters from each sequence.
+   -m, --mark  Document the edit by appending '(uf:take:[but:]NUM)' to headers.
 " >&2
-	exit ${1:-1}
+    exit ${1:-1}
 }
 
 # Parse options
@@ -46,20 +46,20 @@ 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
@@ -72,7 +72,8 @@ 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:take:" (B?"but:":"") N ")" : "") }
-	NR%2==0 { print B ? substr ($0,1,length($0)-N) : substr ($0,1,N) }
-	' "$@"
+    NR%2==1 { print $0 (M ? " (uf:take:" (B?"but:":"") N ")" : "") }
+    NR%2==0 { print B ? substr ($0,1,length($0)-N) : substr ($0,1,N) }
+    ' "$@"
 
+# vim: sts=4:sw=4:et:si:ai
diff --git a/uf-valid b/uf-valid
index 7b132cb..2fa3c9b 100755
--- a/uf-valid
+++ b/uf-valid
@@ -32,7 +32,7 @@ DNA_ALPHABET="ACGTN"
 RNA_ALPHABET="ACGUN"
 NUCL_ALPHABET="ACGTNUKSYMWRBDHV"
 
-# Amino Acids	
+# Amino Acids    
 #  A  alanine               P  proline       
 #  B  aspartate/asparagine  Q  glutamine      
 #  C  cystine               R  arginine      
@@ -46,18 +46,18 @@ NUCL_ALPHABET="ACGTNUKSYMWRBDHV"
 #  L  leucine               X  any
 #  M  methionine            *  translation stop (EXCLUDED)
 #  N  asparagine            -  gap of indeterminate length (EXCLUDED)
-		
+        
 AMINO_ALPHABET="ABCDEFGHIKLMNPQRSTVXWYZ"
 
 # 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 ...]
 
   Validate the sequences in each FILE against the allowed alphabet.  If no FILE
@@ -65,26 +65,26 @@ Usage: $(basename $0) [OPTIONS] [FILE ...]
   copied to standard output.  For invalid sequences, an error message is printed
   to standard error.
 
-  Options
-   -a|--allow CHARS  Validate sequences against the alphabet consisting of CHARS.
-                     May be specified in addition to the synonyms listed below.
-   -i|--ignore-case  Ignore case for allowed CHARS (default for the synonyms).
-   -v|--headers      Validate the syntax of the headers against NCBI conditions.
-   -s|--stop         Stop processing after the first invalid sequence.
-   -k|--keep         Do not drop invalid sequences but copy them to standard out.
-   -q|--quiet        Do not copy standard input to standard output.
+  OPTIONS
+   -a, --allow CHARS  Validate sequences against the alphabet consisting of CHARS.
+                      May be specified in addition to the synonyms listed below.
+   -i, --ignore-case  Ignore case for allowed CHARS (default for the synonyms).
+   -v, --headers      Validate the syntax of the headers against NCBI conditions.
+   -s, --stop         Stop processing after the first invalid sequence.
+   -k, --keep         Do not drop invalid sequences but copy them to standard out.
+   -q, --quiet        Do not copy standard input to standard output.
 
   Synonyms for the usual alphabets (mutually exclusive):
    --dna             Equivalent to: -i -a '$DNA_ALPHABET'
    --rna             Equivalent to: -i -a '$RNA_ALPHABET'
    --nucl            Equivalent to: -i -a '$NUCL_ALPHABET'
-   --amino|--prot    Equivalent to: -i -a '$AMINO_ALPHABET'
+   --amino, --prot   Equivalent to: -i -a '$AMINO_ALPHABET'
 
   CAVEAT: when using --allow with symbols other than characters: the current
   implementation is a simple regex search for the complement of the alphabet,
   so symbols which are regex meta-characters like ., ?, and * need escaping.
 " >&2
-	exit ${1:-1}
+    exit ${1:-1}
 }
 
 # Set defaults
@@ -99,56 +99,56 @@ QUIET=0
 # Parse options
 
 while [ $# -ne 0 -a "$(expr "$1" : '\(.\)..*')" = "-" ]; do
-	case $1 in
-	--allow=*)
-		ALLOW="${ALLOW}${1#"--allow="}"
-		;;
-	-a|--allow)
-		shift
-		ALLOW="${ALLOW}$1"
-		;;
-	--dna)
-		[ -z "$ALLOW" ] || err_exit "option $1 may be followed by --allow but not otherwise combined"
-		ALLOW="$DNA_ALPHABET"
-		IGNORE_CASE=1
-		;;
-	--rna)
-		[ -z "$ALLOW" ] || err_exit "option $1 may be followed by --allow but not otherwise combined"
-		ALLOW="$RNA_ALPHABET"
-		IGNORE_CASE=1
-		;;
-	--nucl)
-		[ -z "$ALLOW" ] || err_exit "option $1 may be followed by --allow but not otherwise combined"
-		ALLOW="$NUCL_ALPHABET"
-		IGNORE_CASE=1
-		;;
-	--amino|--prot)
-		[ -z "$ALLOW" ] || err_exit "option $1 may be followed by --allow but not otherwise combined"
-		ALLOW="$AMINO_ALPHABET"
-		IGNORE_CASE=1
-		;;
-	-i|--ignore*)
-		IGNORE_CASE=1
-		;;
-	-v|--headers)
-		VAL_HEADERS=1
-		;;
-	-s|--stop)
-		STOP_ON_ERR=1
-		;;
-	-k|--keep-errors)
-		KEEP_ERRORS=1
-		;;
-	-q|--quiet)
-		QUIET=1
-		;;
-	--help)
-		usage_exit 0
-		;;
-	*) usage_exit
-		;;
-	esac
-	shift
+    case $1 in
+    --allow=*)
+        ALLOW="${ALLOW}${1#"--allow="}"
+        ;;
+    -a|--allow)
+        shift
+        ALLOW="${ALLOW}$1"
+        ;;
+    --dna)
+        [ -z "$ALLOW" ] || err_exit "option $1 may be followed by --allow but not otherwise combined"
+        ALLOW="$DNA_ALPHABET"
+        IGNORE_CASE=1
+        ;;
+    --rna)
+        [ -z "$ALLOW" ] || err_exit "option $1 may be followed by --allow but not otherwise combined"
+        ALLOW="$RNA_ALPHABET"
+        IGNORE_CASE=1
+        ;;
+    --nucl)
+        [ -z "$ALLOW" ] || err_exit "option $1 may be followed by --allow but not otherwise combined"
+        ALLOW="$NUCL_ALPHABET"
+        IGNORE_CASE=1
+        ;;
+    --amino|--prot)
+        [ -z "$ALLOW" ] || err_exit "option $1 may be followed by --allow but not otherwise combined"
+        ALLOW="$AMINO_ALPHABET"
+        IGNORE_CASE=1
+        ;;
+    -i|--ignore*)
+        IGNORE_CASE=1
+        ;;
+    -v|--headers)
+        VAL_HEADERS=1
+        ;;
+    -s|--stop)
+        STOP_ON_ERR=1
+        ;;
+    -k|--keep-errors)
+        KEEP_ERRORS=1
+        ;;
+    -q|--quiet)
+        QUIET=1
+        ;;
+    --help)
+        usage_exit 0
+        ;;
+    *) usage_exit
+        ;;
+    esac
+    shift
 done
 
 # Check that at least some alphabet was selected
@@ -158,33 +158,34 @@ done
 # Do the work
 
 awk -b -O -v P="$(basename "$0")" -v WRONG="[^$ALLOW]" -v H=$VAL_HEADERS -v Q=$QUIET -v K=$KEEP_ERRORS -v S=$STOP_ON_ERR -v IGNORECASE=$IGNORE_CASE '{
-	ERR = 0
-	HDR = $0
-	if ( HDR !~ /^>/ ) {
-		print P ": no FASTA header found at line " NR
-		ERR = 1
-	} 
-	else if ( H && HDR !~ /^>[[:alpha:]]+\|[[:alnum:]._]+(\|[[:alnum:]._]+)*\|?(\s+.*)?$/ ) {  # rudimentary syntax check of header
-		print P ": invalid header syntax at line " NR ": " HDR > "/dev/stderr"
-		ERR = 1
-	}
-	if ( getline SEQ != 1 ) {
-		print P ": read error or end of file, no sequence read at line " NR
-		ERR = 1
-	}
-	else {
-		POS = match (SEQ, WRONG)
-		if ( POS ) {
-			print P ": invalid character in sequence at line " NR ", pos " POS ": " substr(SEQ,POS,1) > "/dev/stderr"
-			ERR = 1
-		}
-	}
-	if ( (!ERR || K) && !Q ) {
-		print HDR
-		print SEQ
-	}
-	if ( ERR && S ) {
-		exit 1
-	}
+    ERR = 0
+    HDR = $0
+    if ( HDR !~ /^>/ ) {
+        print P ": no FASTA header found at line " NR
+        ERR = 1
+    } 
+    else if ( H && HDR !~ /^>[[:alpha:]]+\|[[:alnum:]._]+(\|[[:alnum:]._]+)*\|?(\s+.*)?$/ ) {  # rudimentary syntax check of header
+        print P ": invalid header syntax at line " NR ": " HDR > "/dev/stderr"
+        ERR = 1
+    }
+    if ( getline SEQ != 1 ) {
+        print P ": read error or end of file, no sequence read at line " NR
+        ERR = 1
+    }
+    else {
+        POS = match (SEQ, WRONG)
+        if ( POS ) {
+            print P ": invalid character in sequence at line " NR ", pos " POS ": " substr(SEQ,POS,1) > "/dev/stderr"
+            ERR = 1
+        }
+    }
+    if ( (!ERR || K) && !Q ) {
+        print HDR
+        print SEQ
+    }
+    if ( ERR && S ) {
+        exit 1
+    }
 }' "$@"
 
+# vim: sts=4:sw=4:et:si:ai