mkarPg8plus:
	run_MKAR.py /human/hg18/align/multiz3way/ cache/pgSnpsCombined8plus.mkar cache/arPonAbeV3 cache/ucscCodingExons.bed 10000 10000 hg18,panTro2 cache/out/pgSnp8plusPanTro/

#filter output for result rows
#cat cache/out/pgSnp8plusPanTro/*.out | perl -ne 'chomp; if (/^chr/) { print "$_\n"; }' > all.mkar

#filter for testable windows
#cat cache/out/pgSnp8plusPanTro/all.mkar | perl -ne 'chomp; split(/\t/); if ($_[10] >= 5 && $_[11] >= 5 && $_[12] >= 5 && $_[13] >= 5) { print join("\t", @_), "\n"; }' > min5.mkar

#fix zero-division by replacing with small number if desired (.0001).

qvals:
	echo 'infile <- "cache/out/pgSnp8plus30kPanTro/min5.fix0.mkar"; outfile <- "cache/out/pgSnp8plus30kPanTro/results.fix0.txt";' | cat - computeQvals.r | R --slave --vanilla

#now filter out significant windows