Merge branch 'develop' of github.com:samtools/bcftools into develop

Author: pd3

convert.c

@@ -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++] = ' ';
             }
@@ -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 */
             {
@@ -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 */
             {
@@ -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 */
             {
@@ -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 */
             {