From ffff1804d14718c13104438e5bdbc12624567e80 Mon Sep 17 00:00:00 2001
From: Alexandr <prowtiger@gmail.com>
Date: Thu, 26 Jan 2017 21:50:12 -0500
Subject: [PATCH] Argument parsing corrections

1. Several arguments were incorrectly converted to integer instead of float
which rounded them. Arguments (like minhetfreq) that were in range (0, 1) were
rounded to 0 and hence always assigned default values during later checks
(BS-SNPer.pl:48-55 @ master)
2. It wasn't possible to set any argument to 0 as in this case in later checks
(BS-SNPer.pl:48-55 @ master) 0 was interpreted as False and the default value
was used in such cases.
3. It doesn't make sense to check @ARGV == 0 here as it will be empty
after GetOptions. What makes sense is checking for files, as there are no
default values for them. Although for output files it might be good idea
to just construct them based on input filename by adding predefined suffixes,
i.e. if $bam == file.bam, $methcg would be file.bam.methcg
---
 BS-Snper.pl | 42 ++++++++++++++++++++++++++++++------------
 1 file changed, 30 insertions(+), 12 deletions(-)

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;