Update @SQ lines during 'samtools depad'

Note does not (yet) preserve additional @SQ line tags (e.g. AS, SP, UR).

diff --git a/padding.c b/padding.c
index 23d1b23c9ac68dd8dd6a5d1c7847d714e3e837ed..b7a254ff69df23fbc99aa05c0c8ec162baa95251 100644 (file)
--- a/padding.c
+++ b/padding.c
@@ -295,10 +295,48 @@ bam_header_t * fix_header(bam_header_t *old, faidx_t *fai)
                        fprintf(stderr, "[depad] ERROR getting unpadded length of '%s', padded length %i\n", old->target_name[i], old->target_len[i]);
                } else {
                        header->target_len[i] = unpadded_len;
-                       fprintf(stderr, "[depad] Recalculating '%s' length %i -> %i\n", old->target_name[i], old->target_len[i], header->target_len[i]);
+                       //fprintf(stderr, "[depad] Recalculating '%s' length %i -> %i\n", old->target_name[i], old->target_len[i], header->target_len[i]);
                }
        }
-       /* TODO - Correct the @SQ reference lengths from padded to unpadded */
+       /* Duplicating the header allocated new buffer for header string */
+       /* After modifying the @SQ lines it will only get smaller, since */
+       /* the LN entries will be the same or shorter, and we'll remove */
+       /* any MD entries (MD5 checksums). */
+       assert(strlen(old->text) == strlen(header->text));
+       assert (0==strcmp(old->text, header->text));
+       const char *text;
+       text = old->text;
+       header->text[0] = '\0'; /* Resuse the allocated buffer */
+       char * newtext = header->text;
+       char * end=NULL;
+       while (text[0]=='@') {
+               end = strchr(text, '\n');
+               assert(end != 0);
+               if (text[1]=='S' && text[2]=='Q' && text[3]=='\t') {
+                       /* TODO - edit the @SQ line here to remove MD and fix LN. */
+                       /* For now just remove the @SQ line, and samtools will */
+                       /* automatically generate a minimal replacement with LN. */
+                       /* However, that discards any other tags like AS, SP, UR. */
+                       //fprintf(stderr, "[depad] Removing @SQ line\n");
+               } else {
+                       /* Copy this line to the new header */
+                       strncat(newtext, text, end - text + 1);
+               }
+               text = end + 1;
+       }
+       assert (text[0]=='\0');
+       /* Check we didn't overflow the buffer */
+       assert (strlen(header->text) <= strlen(old->text));
+       if (strlen(header->text) < header->l_text) {
+               //fprintf(stderr, "[depad] Reallocating header buffer\n");
+               assert (newtext == header->text);
+               newtext = calloc(strlen(header->text) + 1, 1);
+               strcpy(newtext, header->text);
+               free(header->text);
+               header->text = newtext;
+               header->l_text = strlen(newtext);
+       }
+       //fprintf(stderr, "[depad] Here is the new header (pending @SQ lines),\n\n%s\n(end)\n", header->text);
        return header;
 }