From 51ffe3e1edb69af534dea8137d56455b1248f740 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Sun, 5 Dec 2010 04:33:51 +0000 Subject: [PATCH] Fixed a compiling error when knetfile is not used. --- bam_reheader.c | 3 ++- bcftools/vcfutils.pl | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) 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] -- 2.39.2