review update

Author: vasudeva8

vcf.c

@@ -1827,7 +1827,7 @@ static void bcf_record_check_err(const bcf_hdr_t *hdr, bcf1_t *rec,
  */
 static int updatephasing(uint8_t *p, uint8_t *end, uint8_t **q, int set, int samples, int ploidy, int type)
 {
-    int j, k, upd = set ? 1 : -1;
+    int j, k;
     size_t bytes;
     for (j = 0; j < samples; ++j) {   //for each sample
         int anyunphased = 0;
@@ -1839,10 +1839,10 @@ static int updatephasing(uint8_t *p, uint8_t *end, uint8_t **q, int set, int sam
                     val = *(uint8_t*)p;
                 break;
                 case BCF_BT_INT16:
-                    val = *(uint16_t*)p;
+                    val = le_to_i16(p);
                 break;
                 case BCF_BT_INT32:
-                    val = *(uint32_t*)p;
+                    val = le_to_i32(p);
                 break;
                 //wont have anything bigger than 32bit for GT
                 default: //invalid
@@ -1854,26 +1854,28 @@ static int updatephasing(uint8_t *p, uint8_t *end, uint8_t **q, int set, int sam
                 anyunphased = 1;
             }
             //get to next phasing or skip the rest for this sample
-            bytes = (anyunphased ? ploidy - k : 1) << bcf_type_shift[type];
+            bytes = ((anyunphased || al1 & 1) ? ploidy - k : 1) << bcf_type_shift[type];
             if (end - p < bytes)
                 return 1;
             p += bytes;
-            if (anyunphased) {
+            if (anyunphased || al1 & 1) {
+                //either unphased is found or 1st one itself is set as phased
                 break;  //no further check required
             }
         }
         if (!anyunphased && al1 > 1) {  //no other unphased
             /*set phased on read or make unphased on write as upto 4.3 1st
             phasing is not described explicitly and has to be inferred*/
+            al1 = set ? al1 | 1 : al1 & 0xFFFFFFFE;
             switch(type) {
                 case BCF_BT_INT8:
-                    *(uint8_t*)ptr1 += upd;
+                    *(uint8_t*)ptr1 = al1;
                 break;
                 case BCF_BT_INT16:
-                    *(uint16_t*)ptr1 += upd;
+                    i16_to_le(le_to_i16((uint8_t*)&al1), ptr1);
                 break;
                 case BCF_BT_INT32:
-                    *(uint32_t*)ptr1 += upd;
+                    i32_to_le(le_to_i32((uint8_t*)&al1), ptr1);
                 break;
             }
         }
@@ -2442,11 +2444,6 @@ int bcf_write(htsFile *hfp, bcf_hdr_t *h, bcf1_t *v)
         return -1;
     }
 
-    if (update44phasing(h, v, 0)) { //reset phasing update made after read
-        hts_log_error("Failed to set prorper phasing at %s:%"PRIhts_pos"", bcf_seqname_safe(h,v), v->pos+1);
-        return -1;
-    }
-
     BGZF *fp = hfp->fp.bgzf;
     uint8_t x[32];
     u32_to_le(v->shared.l + 24, x); // to include six 32-bit integers