+bam_header_t * fix_header(bam_header_t *old, faidx_t *fai)
+{
+ int i = 0, unpadded_len = 0;
+ bam_header_t *header = 0 ;
+
+ header = bam_header_dup(old);
+ for (i = 0; i < old->n_targets; ++i) {
+ unpadded_len = get_unpadded_len(fai, old->target_name[i], old->target_len[i]);
+ if (unpadded_len < 0) {
+ 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]);
+ }
+ }
+ /* 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 = malloc(strlen(header->text) + 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;
+}
+