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Added check for \t at the end of lines in BED-file
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renewiegandt authored Jan 6, 2019
1 parent b1cab10 commit cca8ac4
Showing 1 changed file with 4 additions and 3 deletions.
7 changes: 4 additions & 3 deletions bin/1.2_filter_motifs/compareBed.sh
Original file line number Diff line number Diff line change
Expand Up @@ -89,7 +89,7 @@ case $key in
esac
done

# stores unknown selected parameters for error report
# stores unknown selected parameters for error report
count=${#wrong[@]}
if [ $count -gt 0 ]
then
Expand Down Expand Up @@ -178,7 +178,7 @@ then
fi

#default path of the scripts merge.R and maxScore.R is the same path as compareBed.sh has
# the `echo $0 | sed 's/\/[^\/]*$/\//g'` command extracts the path from $0, where the command itself is stored
# the `echo $0 | sed 's/\/[^\/]*$/\//g'` command extracts the path from $0, where the command itself is stored
if [ $pa == false ]
then
path=`echo $0 | sed 's/\/[^\/]*$/\//g'`
Expand All @@ -198,6 +198,7 @@ if [ -d "$motifs" ]
then
for i in "$motifs"/*.bed
do
sed -i 's/[ \t]*$//' $i
if [ $help == true ]
then
help=false
Expand Down Expand Up @@ -272,7 +273,7 @@ do
done
fi

#The output of the last iteration of the subtract loop is written to pass2Tr.bed
#The output of the last iteration of the subtract loop is written to pass2Tr.bed
if [ $help == false ]
then
cat "$workdir"/pass1FaHelp.bed > "$workdir"/pass2Tr.bed
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