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#converts a matches file (generated by extractaligned.java) to a bed file. Can also specify a string to search for and only return records with that sequence.
NT=$2
FL=$1
if ["$NT" == ""]; then
grep ">" $FL | sed s/"(-)"/"\tminus"/g | sed s/'-'/"\t"/g | sed s/':'/"\t"/g | sed s/"(+)"/"\t+"/g | sed s/"minus"/"-"/g | sed s/'>'/""/g
else
grep -B 1 "^${NT}$" $FL | grep ">" | sed s/"(-)"/"\tminus"/g | sed s/'-'/"\t"/g | sed s/':'/"\t"/g | sed s/"(+)"/"\t+"/g | sed s/"minus"/"-"/g | sed s/'>'/""/g