diff --git a/BS-Snper.pl b/BS-Snper.pl index 7e58024..30c664d 100644 --- a/BS-Snper.pl +++ b/BS-Snper.pl @@ -34,25 +34,43 @@ =head1 Exmple "methcg:s"=>\$methcg, "methchg:s"=>\$methchg, "methchh:s"=>\$methchh, - "minhetfreq:i"=>\$minhetfreq, - "minhomfreq:i"=>\$minhomfreq, + "minhetfreq:f"=>\$minhetfreq, + "minhomfreq:f"=>\$minhomfreq, "minquali:i"=>\$minquali, "mincover:i"=>\$mincover, "maxcover:i"=>\$maxcover, "minread2:i"=>\$minread2, - "errorate:i"=>\$errorate, + "errorate:f"=>\$errorate, "mapvalue:i"=>\$mapvalue, "help"=>\$Help ); -die `pod2text $0` if (@ARGV==0 || $Help); -$minhetfreq ||=0.1; -$minhomfreq ||=0.85; -$minquali ||=15; -$mincover ||=10; -$minread2 ||=2; -$maxcover ||=1000; -$errorate ||=0.02; -$mapvalue ||=20; +die `pod2text $0` if (not defined $fasta || not defined $bam || + not defined $output || not defined $methcg || not defined $methchg || + not defined $methchh || $Help); +if (not defined $minhetfreq) { + $minhetfreq=0.1; +} +if (not defined $minhomfreq) { + $minhomfreq=0.85; +} +if (not defined $minquali) { + $minquali=15; +} +if (not defined $mincover) { + $mincover=10; +} +if (not defined $minread2) { + $minread2=2; +} +if (not defined $maxcover) { + $maxcover=1000; +} +if (not defined $errorate) { + $errorate=0.02; +} +if (not defined $mapvalue) { + $mapvalue=20; +} #$pvalue ||=0.01; my $eee=2.7;