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

Fix parsing of options and spacing.

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