More review commits

Author: jkbonfield

htslib/vcf.h

@@ -1562,16 +1562,6 @@ static inline int bcf_enc_inttype(long x)
     return BCF_BT_INT32;
 }
 
-// INTERNAL - not to be assumed to be a part of public API
-// As per bcf_enc_size but kstring is already guaranteed to be big enough
-// and with size == 1.
-static inline void bcf_enc_size1_(kstring_t *s, int type)
-{
-        uint8_t *p = (uint8_t *)s->s + s->l;
-        *p++ = (1<<4) | type;
-        s->l++;
-}
-
 static inline int bcf_enc_int1(kstring_t *s, int32_t x)
 {
     if (ks_resize(s, s->l + 5) < 0)

vcf.c

@@ -2487,9 +2487,11 @@ int bcf_enc_vint(kstring_t *s, int n, int32_t *a, int wsize)
 {
     int32_t max = INT32_MIN, min = INT32_MAX;
     int i;
-    if (n <= 0) bcf_enc_size(s, 0, BCF_BT_NULL);
-    else if (n == 1) bcf_enc_int1(s, a[0]);
-    else {
+    if (n <= 0) {
+        return bcf_enc_size(s, 0, BCF_BT_NULL);
+    } else if (n == 1) {
+        return bcf_enc_int1(s, a[0]);
+    } else {
         if (wsize <= 0) wsize = n;
 
         // Equivalent to:
@@ -2528,9 +2530,9 @@ int bcf_enc_vint(kstring_t *s, int n, int32_t *a, int wsize)
         }
 
         if (max <= BCF_MAX_BT_INT8 && min >= BCF_MIN_BT_INT8) {
-            bcf_enc_size(s, wsize, BCF_BT_INT8);
-
-            ks_resize(s, s->l + n);
+            if (bcf_enc_size(s, wsize, BCF_BT_INT8) < 0 ||
+                ks_resize(s, s->l + n) < 0)
+                return -1;
             uint8_t *p = (uint8_t *) s->s + s->l;
             for (i = 0; i < n; ++i, p++) {
                 if ( a[i]==bcf_int32_vector_end )   *p = bcf_int8_vector_end;
@@ -2540,8 +2542,9 @@ int bcf_enc_vint(kstring_t *s, int n, int32_t *a, int wsize)
             s->l += n;
         } else if (max <= BCF_MAX_BT_INT16 && min >= BCF_MIN_BT_INT16) {
             uint8_t *p;
-            bcf_enc_size(s, wsize, BCF_BT_INT16);
-            ks_resize(s, s->l + n * sizeof(int16_t));
+            if (bcf_enc_size(s, wsize, BCF_BT_INT16) < 0 ||
+                ks_resize(s, s->l + n * sizeof(int16_t)) < 0)
+                return -1;
             p = (uint8_t *) s->s + s->l;
             for (i = 0; i < n; ++i)
             {
@@ -2555,8 +2558,9 @@ int bcf_enc_vint(kstring_t *s, int n, int32_t *a, int wsize)
             s->l += n * sizeof(int16_t);
         } else {
             uint8_t *p;
-            bcf_enc_size(s, wsize, BCF_BT_INT32);
-            ks_resize(s, s->l + n * sizeof(int32_t));
+            if (bcf_enc_size(s, wsize, BCF_BT_INT32) < 0 ||
+                ks_resize(s, s->l + n * sizeof(int32_t)) < 0)
+                return -1;
             p = (uint8_t *) s->s + s->l;
             for (i = 0; i < n; ++i) {
                 i32_to_le(a[i], p);
@@ -2566,7 +2570,7 @@ int bcf_enc_vint(kstring_t *s, int n, int32_t *a, int wsize)
         }
     }
 
-    return 0; // FIXME: check for errs in this function
+    return 0;
 }
 
 #ifdef VCF_ALLOW_INT64
@@ -2832,7 +2836,7 @@ static int vcf_parse_format_max3(kstring_t *s, const bcf_hdr_t *h, bcf1_t *v,
         char *r_start = r;
         for (;;) {
             // Quickly skip ahead to an appropriate meta-character
-            while (!meta[(unsigned)*r]) r++;
+            while (!meta[(unsigned char)*r]) r++;
 
             switch (*r) {
             case ',':
@@ -2932,12 +2936,12 @@ static int vcf_parse_format_alloc4(kstring_t *s, const bcf_hdr_t *h, bcf1_t *v,
     return 0;
 }
 
-// fill the sample fields; at beginning of the loop
+// Fill the sample fields
 static int vcf_parse_format_fill5(kstring_t *s, const bcf_hdr_t *h, bcf1_t *v,
                                   const char *p, const char *q, fmt_aux_t *fmt) {
     static int extreme_val_warned = 0;
     int n_sample_ori = -1;
-    // t points to the first char of a format
+    // At beginning of the loop t points to the first char of a format
     const char *t = q + 1;
     int m = 0;   // m: sample id
     const int nsamples = bcf_hdr_nsamples(h);