Patched the example makefile to not use samtools pileup, deprecated.

[samtools.git] / bam_import.c

diff --git a/bam_import.c b/bam_import.c
index 9d463d102bbb254ddf5a5b9bf32b5f216aac2187..29516c92ff42593313caf2833c38213d62ebdc52 100644 (file)
--- a/bam_import.c
+++ b/bam_import.c
@@ -116,7 +116,7 @@ static bam_header_t *hash2header(const kh_ref_t *hash)
 bam_header_t *sam_header_read2(const char *fn)
 {
        bam_header_t *header;
-       int c, dret, ret;
+       int c, dret, ret, error = 0;
        gzFile fp;
        kstream_t *ks;
        kstring_t *str;
@@ -135,6 +135,10 @@ bam_header_t *sam_header_read2(const char *fn)
                ks_getuntil(ks, 0, str, &dret);
                len = atoi(str->s);
                k = kh_put(ref, hash, s, &ret);
+               if (ret == 0) {
+                       fprintf(stderr, "[sam_header_read2] duplicated sequence name: %s\n", s);
+                       error = 1;
+               }
                kh_value(hash, k) = (uint64_t)len<<32 | i;
                if (dret != '\n')
                        while ((c = ks_getc(ks)) != '\n' && c != -1);
@@ -143,6 +147,7 @@ bam_header_t *sam_header_read2(const char *fn)
        gzclose(fp);
        free(str->s); free(str);
        fprintf(stderr, "[sam_header_read2] %d sequences loaded.\n", kh_size(hash));
+       if (error) return 0;
        header = hash2header(hash);
        kh_destroy(ref, hash);
        return header;
@@ -163,9 +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;
@@ -407,6 +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;
                }