#Single-End read mapping in stampy- for loop
#Written by E Heppenheimer, Summer 2017  

#assumes the files you want to map are named prefix.1.1.fq.gz 

FILES=*1.fq.gz

for f in $FILES
do
pre=$(echo $f |awk -F'.' '{print $1"\n"}')
suf=".sam"

/path/to/stampy.pystampy.py -g /path/to/index -h /path/to/hash -o $pre$suf -M $f
 
done