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

#This loop will properly match read pairs (assuming you have several distinct read pairs you would like to map in one directory)
#This particular set of commands assumes the read names have the same prefix, followed by either ".1.1.fq.gz" or ".2.2.fq.gz" 
#You can either alter this expectations in the code, or rename your files so they follow this convention 

#See Stampy documentation for info on generating index and hash files
#as of April 2018, that info was available here: http://www.well.ox.ac.uk/~gerton/README.txt

#assuming the working directory contains many read pair files with above naming conventions: 
FILES=*1.fq.gz

for f in $FILES
do
 pre=$(echo $f |awk -F'.' '{print $1"\n"}')
 suf=".sam"
 f2="${f/.1.1./.2.2.}"
  
/path/to/stampy.py -g /path/to/index -h /path/to/hash -o $pre$suf -M $f $f2
 
done