Fixed warning about unphased SNPs

Code was checking if a SNP is unphased and if the warn_phase flag is
set in the same conditional.

After unsetting warn_phase, this test would fail, causing additional
unphased SNPs to be converted to missing data.

By creating two separate conditionals, a single warning is printed and
all additional unphased SNPs are parsed normally.

snp2h5/vcf.c

@@ -172,11 +172,13 @@ void vcf_parse_haplotypes(VCFInfo *vcf_info, char *haplotypes,
  /* try with '/' separator instead */
  n = sscanf(inner_tok, "%d/%d", &hap1, &hap2);
 
- if(n == 2 && warn_phase) {
- my_warn("%s:%d: some genotypes are unphased (delimited "
- "with '/' instead of '|')\n", __FILE__, __LINE__,
- inner_tok);
- warn_phase = FALSE;
+ if(n == 2) {
+ if(warn_phase) {
+ my_warn("%s:%d: some genotypes are unphased (delimited "
+ "with '/' instead of '|')\n", __FILE__, __LINE__,
+ inner_tok);
+ warn_phase = FALSE;
+ }
  } else {
  my_warn("%s:%d: could not parse genotype string '%s'\n",
  __FILE__, __LINE__, inner_tok);