Commit 08d9f08a authored by Venkat Malladi's avatar Venkat Malladi
Browse files

Fix parsing of options and spacing.

parent 54b9865d
...@@ -18,15 +18,15 @@ raise() ...@@ -18,15 +18,15 @@ raise()
} }
check_tools() { check_tools() {
raise " raise "
Checking for required libraries and components on this system Checking for required libraries and components on this system
" "
deeptools --version &> version_deeptools.txt deeptools --version &> version_deeptools.txt
if [ $? -gt 0 ] if [ $? -gt 0 ]
then then
raise "Missing deeptools" raise "Missing deeptools"
return 1 return 1
fi fi
} }
compute_matrix() { compute_matrix() {
...@@ -34,13 +34,13 @@ compute_matrix() { ...@@ -34,13 +34,13 @@ compute_matrix() {
Computing matrix on ${1} using ${2} Computing matrix on ${1} using ${2}
" "
computeMatrix reference-point \ computeMatrix reference-point \
--referencePoint TSS \ --referencePoint TSS \
-S ${1} \ -S ${1} \
-R ${2} \ -R ${2} \
--skipZeros \ --skipZeros \
-o computeMatrix.gz \ -o computeMatrix.gz \
-p max/2 -p max/2
if [ $? -gt 0 ] if [ $? -gt 0 ]
then then
...@@ -54,8 +54,8 @@ plot_profile() { ...@@ -54,8 +54,8 @@ plot_profile() {
Plotting profile Plotting profile
" "
plotProfile -m computeMatrix.gz \ plotProfile -m computeMatrix.gz \
-out plotProfile.png -out plotProfile.png
if [ $? -gt 0 ] if [ $? -gt 0 ]
then then
...@@ -69,7 +69,7 @@ run_main() { ...@@ -69,7 +69,7 @@ run_main() {
# Parsing options # Parsing options
OPTIND=1 # Reset OPTIND OPTIND=1 # Reset OPTIND
while getopts :gh opt while getopts :g:h opt
do do
case $opt in case $opt in
g) gtf=$OPTARG;; g) gtf=$OPTARG;;
...@@ -84,20 +84,20 @@ run_main() { ...@@ -84,20 +84,20 @@ run_main() {
usage usage
fi fi
bws=$(ls *.bw) bws=$(ls *.bw)
check_tools || exit 1 check_tools || exit 1
compute_matrix "${bws}" "${gtf}" || return 1 compute_matrix "${bws}" "${gtf}" || return 1
plot_profile || return 1 plot_profile || return 1
raise "ALL COMPLETE" raise "ALL COMPLETE"
} }
if [[ "${BASH_SOURCE[0]}" == "${0}" ]] if [[ "${BASH_SOURCE[0]}" == "${0}" ]]
then then
run_main run_main "$@"
if [ $? -gt 0 ] if [ $? -gt 0 ]
then then
exit 1 exit 1
......
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