fprintf(stderr, "\n");
fprintf(stderr, "Usage: bamtk tview [options] <aln.bam> [ref.fasta]\n");
fprintf(stderr, "Options:\n");
+ fprintf(stderr, " -d display output as (H)tml or (C)urses or (T)ext \n");
fprintf(stderr, " -p chr:pos go directly to this position\n");
fprintf(stderr, " -s STR display only reads from this sample or group\n");
- fprintf(stderr, " -d display (H)tml or (C)urses or (T)ext \n");
fprintf(stderr, "\n\n");
}
else
vc.sublist = calloc(vc.n_sub, sizeof(int));
hout = bcf_hdr_subsam(hin, vc.n_sub, vc.subsam, vc.sublist);
}
- if (vc.flag & VC_CALL) write_header(hout);
+ write_header(hout); // always print the header
vcf_hdr_write(bout, hout);
}
if (vc.flag & VC_CALL) {