From: Heng Li <lh3@live.co.uk>
Date: Wed, 3 Nov 2010 19:51:24 +0000 (+0000)
Subject: fixed a minor problem in the example coming with kprobaln.c
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=48c105217263ffe19b676f6f6c918dc1c6f39c88;p=samtools.git

fixed a minor problem in the example coming with kprobaln.c
---

diff --git a/bcftools/vcfutils.pl b/bcftools/vcfutils.pl
index d0b7971..e2c3107 100755
--- a/bcftools/vcfutils.pl
+++ b/bcftools/vcfutils.pl
@@ -155,7 +155,7 @@ Note: This command discards indels. Output: QUAL #non-indel #SNPs #transitions #
 	next if (length($t[3]) != 1 || uc($t[3]) eq 'N');
 	$t[3] = uc($t[3]); $t[4] = uc($t[4]);
 	my @s = split(',', $t[4]);
-	$t[5] = 3 if ($t[5] < 0);
+	$t[5] = 3 if ($t[5] eq '.' || $t[5] < 0);
 	next if (length($s[0]) != 1);
 	my $hit;
 	if ($is_vcf) {
diff --git a/kprobaln.c b/kprobaln.c
index 1a3d7b6..c3d05dd 100644
--- a/kprobaln.c
+++ b/kprobaln.c
@@ -285,7 +285,7 @@ int main(int argc, char *argv[])
 	iqual = malloc(l_query);
 	memset(iqual, q, l_query);
 	kpa_par_def.bw = b;
-	kpa_glocal(ref, l_ref, query, l_query, iqual, &kpa_par_def, 0, 0, 0);
+	kpa_glocal(ref, l_ref, query, l_query, iqual, &kpa_par_def, 0, 0);
 	free(iqual);
 	return 0;
 }