Shell Programming and Scripting

Hello all,

I wrote this command line for some calculation on my given input files based on another input file which is a txt file.

Code:

while read BAM REGION;  do samtools view $BAM $REGION | awk '{if ($2==0) print $0}' | wc -l  >>log.txt; echo "$REGION"; done >> log.txt <regions.txt

It takes each file and parse it and with wc -l I want to count the number of lines and writing to output file.
My problem is that it writes $REGION and calculation of samtools in separate lines. It gives me the output like this:


But I want it to be like this:


Can you help me with this?
Thanks for your consideration.

You can print both variables in awk itself...

Code:

while read BAM REGION;  
do
var=$(vasamtools view $BAM $REGION | awk '{if ($2==0) print $0}' | wc -l)
echo "$REGION $var" >> log.txt
done<regions.txtt

Thanks man. But now it doesn't give me the $REGION in output. Since you put it before wc whatever it write it just counts the line after pipe. now the output is just the calcs.
I think writing the regions should be after wc -l or maybe we should think to count the lines in another way... I don't know! :\

Yeah just corrected the code. Please check now..

I tried your correction several times and it gave me zero values for all my calcs. AS ALWAYS, suddenly it started working! I really don't know what happens sometimes!! But now it's working! Thanks man!