command help

run-fermi.pl

@@ -9,8 +9,17 @@
 sub main {
 	my %opts = (e=>'fermi', t=>2, p=>'fmdef', f=>17, k=>50);
 	getopts('e:t:p:Pcf:', \%opts);
-
-	die(qq/Usage: run-fermi.pl [options] <in1.fq> [in2.fq [...]]\n/) if (@ARGV == 0);
+	$opts{P} = 1 if defined($opts{c});
+
+	die(qq/
+Usage:   run-fermi.pl [options] <in1.fq> [in2.fq [...]]\n
+Options: -P        the input is paired
+         -c        the input is collated FASTQ (two ends in the same file)
+         -t INT    number of threads [$opts{t}]
+         -p STR    prefix of output files [$opts{p}]
+         -f INT    k-mer length for unique-mer filtering [$opts{f}]
+         -k INT    minimum overlap [$opts{k}]
+\n/) if (@ARGV == 0);
 
 	my (@lines, $in_list, $fqs);