corrected the wrong stats output of number of footprints after filter

[JannikHamp]

wrong file was chosen. filtered_flagged.bed is the corresct one instead of filtered.bed

[renewiegandt]

Please set the target branch to dev. We do not merge directly into the master branch.

[renewiegandt]

I tested the changes.
It is close but not correct. In the test output file, I generated are 807 footprints.
In the stats it tells me it has 806 footprints. Could it be that you subtract 1 of the total number of footprints?

[renewiegandt]

See comment.
If you write a header to the temp-files depending on parameters or other factors, please check if the header exists before subtracting 1.

[renewiegandt]

Please remove the -1 from line 283. Since you are not writing a header to this temp-file you do not need to subtract 1.

[renewiegandt]

I think what you are doing is not quite correct.
You check if the input file has got a header. If it does you write the header to your output file. Then you count the lines from your temp-file and subtract 1. But your temp-fille does not contain a header only your in- and output file.
You can do following:
Instead of:

# check if header existed. If so, final output also has a header.
first_line=`sed -n 1p $data | sed "s/$/\tcontains_maxpos\tsequence/"`
if [[ ${first_line:0:1} == "#" ]]
then
	echo "$first_line" > $output
	# add some final values to the log file
	fp_initial=`cat $data | wc -l`
	fp_initial=`expr $fp_initial - 1`
	fp_final=`cat "$workdir"/filtered_flagged.bed | wc -l`
	fp_final=`expr $fp_final - 1`
	echo $fp_initial | sed 's/^/initial number of footprints: /g' >> "$workdir"/compareBed.stats
	echo $fp_final | sed 's/^/number of footprints after subtract: /g' >> "$workdir"/compareBed.stats
else
	# output will be overwritten if it exists
	rm -f $output
	# add some final values to the log file
	cat $data | wc -l | sed 's/^/initial number of footprints: /g' >> "$workdir"/compareBed.stats
	cat "$workdir"/filtered_flagged.bed | wc -l | sed 's/^/number of footprints after subtract: /g' >> "$workdir"/compareBed.stats
fi

do this:

# check if header existed. If so, final output also has a header.
first_line=`sed -n 1p $data | sed "s/$/\tcontains_maxpos\tsequence/"`
if [[ ${first_line:0:1} == "#" ]]
then
	echo "$first_line" > $output
fi
# output will be overwritten if it exists
rm -f $output
# add some final values to the log file
cat $data | wc -l | sed 's/^/initial number of footprints: /g' >> "$workdir"/compareBed.stats
cat "$workdir"/filtered_flagged.bed | wc -l | sed 's/^/number of footprints after subtract: /g' >> "$workdir"/compareBed.stats

[JannikHamp]

I changed the script. Thanks for finding this little bug

[renewiegandt]

Ok, the numbers match now.