X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_import.c;h=29516c92ff42593313caf2833c38213d62ebdc52;hb=80658e4d152b53bd55927c432ceece7702ab49d7;hp=3a4a5cdf64611d1aa23e98b703976fc85beda117;hpb=9215c0998a15d7ebc82baf78ded2443c55a1bc93;p=samtools.git

diff --git a/bam_import.c b/bam_import.c
index 3a4a5cd..29516c9 100644
--- a/bam_import.c
+++ b/bam_import.c
@@ -168,9 +168,24 @@ static inline void parse_error(int64_t n_lines, const char * __restrict msg)
 }
 static inline void append_text(bam_header_t *header, kstring_t *str)
 {
-	int x = header->l_text, y = header->l_text + str->l + 2; // 2 = 1 byte dret + 1 byte null
+	size_t x = header->l_text, y = header->l_text + str->l + 2; // 2 = 1 byte dret + 1 byte null
 	kroundup32(x); kroundup32(y);
-	if (x < y) header->text = (char*)realloc(header->text, y);
+	if (x < y) 
+    {
+        header->n_text = y;
+        header->text = (char*)realloc(header->text, y);
+        if ( !header->text ) 
+        {
+            fprintf(stderr,"realloc failed to alloc %ld bytes\n", y);
+            abort();
+        }
+    }
+    // Sanity check
+    if ( header->l_text+str->l+1 >= header->n_text )
+    {
+        fprintf(stderr,"append_text FIXME: %ld>=%ld, x=%ld,y=%ld\n",  header->l_text+str->l+1,header->n_text,x,y);
+        abort();
+    }
 	strncpy(header->text + header->l_text, str->s, str->l+1); // we cannot use strcpy() here.
 	header->l_text += str->l + 1;
 	header->text[header->l_text] = 0;
@@ -412,6 +427,27 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
 				memcpy(s, str->s + 5, str->l - 5);
 				s[str->l - 5] = 0;
 				doff += size;
+			} else if (type == 'B') {
+				int32_t n = 0, Bsize, k = 0, size;
+				char *p;
+				if (str->l < 8) parse_error(fp->n_lines, "too few values in aux type B");
+				Bsize = bam_aux_type2size(str->s[5]); // the size of each element
+				for (p = (char*)str->s + 6; *p; ++p) // count the number of elements in the array
+					if (*p == ',') ++n;
+				p = str->s + 7; // now p points to the first number in the array
+				size = 6 + Bsize * n; // total number of bytes allocated to this tag
+				s = alloc_data(b, doff + 6 * Bsize * n) + doff; // allocate memory
+				*s++ = 'B'; *s++ = str->s[5];
+				memcpy(s, &n, 4); s += 4; // write the number of elements
+				if (str->s[5] == 'c')      while (p < str->s + str->l) ((int8_t*)s)[k++]   = (int8_t)strtol(p, &p, 0),   ++p;
+				else if (str->s[5] == 'C') while (p < str->s + str->l) ((uint8_t*)s)[k++]  = (uint8_t)strtol(p, &p, 0),  ++p;
+				else if (str->s[5] == 's') while (p < str->s + str->l) ((int16_t*)s)[k++]  = (int16_t)strtol(p, &p, 0),  ++p; // FIXME: avoid unaligned memory
+				else if (str->s[5] == 'S') while (p < str->s + str->l) ((uint16_t*)s)[k++] = (uint16_t)strtol(p, &p, 0), ++p;
+				else if (str->s[5] == 'i') while (p < str->s + str->l) ((int32_t*)s)[k++]  = (int32_t)strtol(p, &p, 0),  ++p;
+				else if (str->s[5] == 'I') while (p < str->s + str->l) ((uint32_t*)s)[k++] = (uint32_t)strtol(p, &p, 0), ++p;
+				else if (str->s[5] == 'f') while (p < str->s + str->l) ((float*)s)[k++]    = (float)strtod(p, &p),       ++p;
+				else parse_error(fp->n_lines, "unrecognized array type");
+				s += Bsize * n; doff += size;
 			} else parse_error(fp->n_lines, "unrecognized type");
 			if (dret == '\n' || dret == '\r') break;
 		}