use while -v loop instead of for arg in

this is more robust and doesn't require extra handling

Author: wookietreiber

diamonddb.sh

@@ -89,17 +89,9 @@ syslog=no
 debug=no
 verbose=no
 
-ignore_next_arg=no
-
-for arg in "$@"
+while [[ -v 1 ]]
 do
-  if [[ $ignore_next_arg == yes ]]
-  then
-    ignore_next_arg=no
-    continue
-  fi
-
-  case "$arg" in
+  case "$1" in
     -\?|--help)
       usage
       exit
@@ -115,7 +107,6 @@ do
       cores=${1:?"parallel option has no argument"}
       [[ $cores =~ ^[0-9]+$ ]] ||
         bailout "parallel option argument is not a number: $cores"
-      ignore_next_arg=yes
       shift
       ;;
 
@@ -145,7 +136,7 @@ do
       ;;
 
     --debug=yes|--debug=no)
-      debug=${arg##--debug=}
+      debug=${1##--debug=}
       shift
       ;;
 
@@ -161,7 +152,7 @@ do
       ;;
 
     --verbose=yes|--verbose=no)
-      verbose=${arg##--verbose=}
+      verbose=${1##--verbose=}
       shift
       ;;
 
@@ -171,7 +162,7 @@ do
       ;;
 
     -*)
-      bailout "unrecognized option: $arg"
+      bailout "unrecognized option: $1"
       ;;
 
     *)

ebidl.sh

@@ -79,17 +79,9 @@ syslog=no
 debug=no
 verbose=no
 
-ignore_next_arg=no
-
-for arg in "$@"
+while [[ -v 1 ]]
 do
-  if [[ $ignore_next_arg == yes ]]
-  then
-    ignore_next_arg=no
-    continue
-  fi
-
-  case "$arg" in
+  case "$1" in
     -\?|--help)
       usage
       exit
@@ -105,7 +97,6 @@ do
       cores=${1:?"parallel option has no argument"}
       [[ $cores =~ ^[0-9]+$ ]] ||
         bailout "parallel option argument is not a number: $cores"
-      ignore_next_arg=yes
       shift
       ;;
 
@@ -135,7 +126,7 @@ do
       ;;
 
     --debug=yes|--debug=no)
-      debug=${arg##--debug=}
+      debug=${1##--debug=}
       shift
       ;;
 
@@ -151,7 +142,7 @@ do
       ;;
 
     --verbose=yes|--verbose=no)
-      verbose=${arg##--verbose=}
+      verbose=${1##--verbose=}
       shift
       ;;
 
@@ -161,7 +152,7 @@ do
       ;;
 
     -*)
-      bailout "unrecognized option: $arg"
+      bailout "unrecognized option: $1"
       ;;
 
     *)

ensembldl.sh

@@ -81,17 +81,9 @@ debug=no
 verbose=no
 ensembl_server="ensembl"
 
-ignore_next_arg=no
-
-for arg in "$@"
+while [[ -v 1 ]]
 do
-  if [[ $ignore_next_arg == yes ]]
-  then
-    ignore_next_arg=no
-    continue
-  fi
-
-  case "$arg" in
+  case "$1" in
     -\?|--help)
       usage
       exit
@@ -112,7 +104,6 @@ do
       cores=${1:?"parallel option has no argument"}
       [[ $cores =~ ^[0-9]+$ ]] ||
         bailout "parallel option argument is not a number: $cores"
-      ignore_next_arg=yes
       shift
       ;;
 
@@ -142,7 +133,7 @@ do
       ;;
 
     --debug=yes|--debug=no)
-      debug=${arg##--debug=}
+      debug=${1##--debug=}
       shift
       ;;
 
@@ -158,7 +149,7 @@ do
       ;;
 
     --verbose=yes|--verbose=no)
-      verbose=${arg##--verbose=}
+      verbose=${1##--verbose=}
       shift
       ;;
 
@@ -168,7 +159,7 @@ do
       ;;
 
     -*)
-      bailout "unrecognized option: $arg"
+      bailout "unrecognized option: $1"
       ;;
 
     *)

ncbidl.sh

@@ -79,17 +79,9 @@ syslog=no
 debug=no
 verbose=no
 
-ignore_next_arg=no
-
-for arg in "$@"
+while [[ -v 1 ]]
 do
-  if [[ $ignore_next_arg == yes ]]
-  then
-    ignore_next_arg=no
-    continue
-  fi
-
-  case "$arg" in
+  case "$1" in
     -\?|--help)
       usage
       exit
@@ -105,7 +97,6 @@ do
       cores=${1:?"parallel option has no argument"}
       [[ $cores =~ ^[0-9]+$ ]] ||
         bailout "parallel option argument is not a number: $cores"
-      ignore_next_arg=yes
       shift
       ;;
 
@@ -135,7 +126,7 @@ do
       ;;
 
     --debug=yes|--debug=no)
-      debug=${arg##--debug=}
+      debug=${1##--debug=}
       shift
       ;;
 
@@ -151,7 +142,7 @@ do
       ;;
 
     --verbose=yes|--verbose=no)
-      verbose=${arg##--verbose=}
+      verbose=${1##--verbose=}
       shift
       ;;
 
@@ -161,7 +152,7 @@ do
       ;;
 
     -*)
-      bailout "unrecognized option: $arg"
+      bailout "unrecognized option: $1"
       ;;
 
     *)

ucscdl.sh

@@ -79,17 +79,9 @@ syslog=no
 debug=no
 verbose=no
 
-ignore_next_arg=no
-
-for arg in "$@"
+while [[ -v 1 ]]
 do
-  if [[ $ignore_next_arg == yes ]]
-  then
-    ignore_next_arg=no
-    continue
-  fi
-
-  case "$arg" in
+  case "$1" in
     -\?|--help)
       usage
       exit
@@ -105,7 +97,6 @@ do
       cores=${1:?"parallel option has no argument"}
       [[ $cores =~ ^[0-9]+$ ]] ||
         bailout "parallel option argument is not a number: $cores"
-      ignore_next_arg=yes
       shift
       ;;
 
@@ -135,7 +126,7 @@ do
       ;;
 
     --debug=yes|--debug=no)
-      debug=${arg##--debug=}
+      debug=${1##--debug=}
       shift
       ;;
 
@@ -151,7 +142,7 @@ do
       ;;
 
     --verbose=yes|--verbose=no)
-      verbose=${arg##--verbose=}
+      verbose=${1##--verbose=}
       shift
       ;;
 
@@ -161,7 +152,7 @@ do
       ;;
 
     -*)
-      bailout "unrecognized option: $arg"
+      bailout "unrecognized option: $1"
       ;;
 
     *)

uniprotdl.sh

@@ -79,17 +79,9 @@ syslog=no
 debug=no
 verbose=no
 
-ignore_next_arg=no
-
-for arg in "$@"
+while [[ -v 1 ]]
 do
-  if [[ $ignore_next_arg == yes ]]
-  then
-    ignore_next_arg=no
-    continue
-  fi
-
-  case "$arg" in
+  case "$1" in
     -\?|--help)
       usage
       exit
@@ -105,7 +97,6 @@ do
       cores=${1:?"parallel option has no argument"}
       [[ $cores =~ ^[0-9]+$ ]] ||
         bailout "parallel option argument is not a number: $cores"
-      ignore_next_arg=yes
       shift
       ;;
 
@@ -135,7 +126,7 @@ do
       ;;
 
     --debug=yes|--debug=no)
-      debug=${arg##--debug=}
+      debug=${1##--debug=}
       shift
       ;;
 
@@ -151,7 +142,7 @@ do
       ;;
 
     --verbose=yes|--verbose=no)
-      verbose=${arg##--verbose=}
+      verbose=${1##--verbose=}
       shift
       ;;
 
@@ -161,7 +152,7 @@ do
       ;;
 
     -*)
-      bailout "unrecognized option: $arg"
+      bailout "unrecognized option: $1"
       ;;
 
     *)