lib/bio/db/blast.rb in bio-polyploid-tools-0.8.4 vs lib/bio/db/blast.rb in bio-polyploid-tools-0.8.5

@@ -77,10 +77,12 @@
 	end
 
 	def self.align(opts={})
 		target=opts[:target]
 		query=opts[:query]
-		cmdline = "blastn -query #{query} -db #{target} -outfmt '6 qseqid qstart qend qframe sseqid sstart send sframe score pident qlen slen qseq sseq'"
+		max_target_seqs = 15
+		max_target_seqs = opts[:max_hits] + 1 if opts[:max_hits]
+		cmdline = "blastn -max_target_seqs #{max_target_seqs} -query #{query} -db #{target} -outfmt '6 qseqid qstart qend qframe sseqid sstart send sframe score pident qlen slen qseq sseq'"
 
 		status, stdout, stderr = systemu cmdline
 		if status.exitstatus == 0
 			alns = Array.new unless block_given?
 			stdout.each_line do |e_l|