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Ignore first phasing bit in process_gt_to_hap / process_gt_to_hap2 #2443

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Merged
merged 1 commit into from
Aug 12, 2025
Merged

Ignore first phasing bit in process_gt_to_hap / process_gt_to_hap2 #2443

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12 changes: 6 additions & 6 deletions convert.c
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Original file line number Diff line number Diff line change
Expand Up @@ -878,15 +878,15 @@ static void process_gt_to_hap(convert_t *convert, bcf1_t *line, fmt_t *fmt, int
ptr += fmt_gt->n;
if ( fmt_gt->n==1 ) // haploid genotypes
{
if ( ptr[0]==2 ) /* 0 */
if ( ( ptr[0] >> 1 )==1 ) /* 0 */
{
str->s[str->l++] = '0'; str->s[str->l++] = ' '; str->s[str->l++] = '-'; str->s[str->l++] = ' ';
}
else if ( ptr[0]==bcf_int8_missing ) /* . */
{
str->s[str->l++] = '?'; str->s[str->l++] = ' '; str->s[str->l++] = '?'; str->s[str->l++] = ' ';
}
else if ( ptr[0]==4 ) /* 1 */
else if ( ( ptr[0] >> 1 )==2 ) /* 1 */
{
str->s[str->l++] = '1'; str->s[str->l++] = ' '; str->s[str->l++] = '-'; str->s[str->l++] = ' ';
}
Expand All @@ -895,7 +895,7 @@ static void process_gt_to_hap(convert_t *convert, bcf1_t *line, fmt_t *fmt, int
kputw(bcf_gt_allele(ptr[0]),str); str->s[str->l++] = ' '; str->s[str->l++] = '-'; str->s[str->l++] = ' ';
}
}
else if ( ptr[0]==2 )
else if ( ( ptr[0] >> 1 )==1 )
{
if ( ptr[1]==3 ) /* 0|0 */
{
Expand Down Expand Up @@ -934,7 +934,7 @@ static void process_gt_to_hap(convert_t *convert, bcf1_t *line, fmt_t *fmt, int
str->s[str->l++] = '*'; str->s[str->l++] = ' ';
}
}
else if ( ptr[0]==4 )
else if ( ( ptr[0] >> 1 )==2 )
{
if ( ptr[1]==3 ) /* 1|0 */
{
Expand Down Expand Up @@ -1028,7 +1028,7 @@ static void process_gt_to_hap2(convert_t *convert, bcf1_t *line, fmt_t *fmt, int
for (i=0; i<convert->nsamples; i++)
{
ptr += fmt_gt->n;
if ( ptr[0]==2 )
if ( ( ptr[0] >> 1 )==1 )
{
if ( ptr[1]==3 ) /* 0|0 */
{
Expand Down Expand Up @@ -1067,7 +1067,7 @@ static void process_gt_to_hap2(convert_t *convert, bcf1_t *line, fmt_t *fmt, int
str->s[str->l++] = '*'; str->s[str->l++] = ' ';
}
}
else if ( ptr[0]==4 )
else if ( ( ptr[0] >> 1 )==2 )
{
if ( ptr[1]==3 ) /* 1|0 */
{
Expand Down
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