Ignore first phasing bit in process_gt_to_hap / process_gt_to_hap2

HTSlib version 1.22 introduced prefixed phasing support for VCF
files with version 4.4 or later.  Prior to this the first GT phase
(when reading VCF) was always zero; after it is set either
explicitly or when all other alleles are phased.  This updates
process_gt_to_hap() and process_gt_to_hap2() to ignore the first
phase bit, removing an assumption it is always zero.

Fixes incorrect reporting of phase when using HTSlib 1.22 to read
VCF files with version 4.4 or 4.5.

Author: daviesrob

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 */
             {