### Supplementary Data 8: DNA coverage estimation ###

#! /bin/bash
#-# DNA coverage estimation.
#-# Prog required: soap.coverage2.7.7

###########################
# Define global variables #
###########################

thread=5 #number of threads
spe=Ndegeerella #species name
lib=(37850 37851 37852 37853) #libraries to assemble
kmer=63 #k-mer size
assf=AssemblyOutputs #denovo assembly folder
mapf=MappingOutputs #mapping folder
covf=CovOutputs #coverage folder

#########
# Start #
#########

for (( i = 0; i < ${#lib[@]}; i++ ))
do
	#-1-# Get only uniquely mapped reads for each library
	grep -vw "XS:i" ${mapf}/${spe}_${kmer}.final.soap.sspace.cap_${lib[i]}.sam > ${mapf}/${spe}_${kmer}.final.soap.sspace.cap_${lib[i]}_unique.sam


	#-2-# Compute the DNA coverage with soap coverage for each library
	~/bin/soap.coverage2.7.7/soap.coverage -sam -cvg -i ${mapf}/${spe}_${kmer}.final.soap.sspace.cap_${lib[i]}_unique.sam -onlyuniq -p ${thread} -refsingle ${assf}/${spe}_${kmer}.final.soap.sspace.cap.fasta -o ${covf}/${spe}_${kmer}.final.soap.sspace.cap_${lib[i]}_unique.soapcov
done

#######
# End #
#######