From: Heng Li <lh3@live.co.uk>
Date: Sun, 5 Dec 2010 04:33:51 +0000 (+0000)
Subject: Fixed a compiling error when knetfile is not used.
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=51ffe3e1edb69af534dea8137d56455b1248f740;p=samtools.git

Fixed a compiling error when knetfile is not used.
---

diff --git a/bam_reheader.c b/bam_reheader.c
index bae97c7..0b52267 100644
--- a/bam_reheader.c
+++ b/bam_reheader.c
@@ -22,10 +22,11 @@ int bam_reheader(BGZF *in, const bam_header_t *h, int fd)
 	}
 #ifdef _USE_KNETFILE
 	while ((len = knet_read(in->x.fpr, buf, BUF_SIZE)) > 0)
+		fwrite(buf, 1, len, fp->x.fpw);
 #else
 	while (!feof(in->file) && (len = fread(buf, 1, BUF_SIZE, in->file)) > 0)
+		fwrite(buf, 1, len, fp->file);
 #endif
-		fwrite(buf, 1, len, fp->x.fpw);
 	free(buf);
 	fp->block_offset = in->block_offset = 0;
 	bgzf_close(fp);
diff --git a/bcftools/vcfutils.pl b/bcftools/vcfutils.pl
index 499a4e4..3e5b7b2 100755
--- a/bcftools/vcfutils.pl
+++ b/bcftools/vcfutils.pl
@@ -455,7 +455,7 @@ sub hapmap2vcf {
 }
 
 sub vcf2fq {
-  my %opts = (d=>3, D=>100000, Q=>10, l=>10);
+  my %opts = (d=>3, D=>100000, Q=>10, l=>5);
   getopts('d:D:Q:l:', \%opts);
   die(qq/
 Usage:   vcfutils.pl vcf2fq [options] <all-site.vcf>