- bh->txt = malloc(strlen(BAM_VERSION) + 64);
- bh->l_txt = 1 + sprintf(bh->txt, "##samtoolsVersion=%s\n", BAM_VERSION);
- free(s.s);
+ s.l = 0;
+ ksprintf(&s, "##samtoolsVersion=%s\n", BAM_VERSION);
+ if (conf->fai_fname) ksprintf(&s, "##reference=file://%s\n", conf->fai_fname);
+ h->dict = sam_header_parse2(h->text);
+ int nseq;
+ const char *tags[] = {"SN","LN","UR","M5",NULL};
+ char **tbl = sam_header2tbl_n(h->dict, "SQ", tags, &nseq);
+ for (i=0; i<nseq; i++)
+ {
+ ksprintf(&s, "##contig=<ID=%s", tbl[4*i]);
+ if ( tbl[4*i+1] ) ksprintf(&s, ",length=%s", tbl[4*i+1]);
+ if ( tbl[4*i+2] ) ksprintf(&s, ",URL=%s", tbl[4*i+2]);
+ if ( tbl[4*i+3] ) ksprintf(&s, ",md5=%s", tbl[4*i+3]);
+ kputs(">\n", &s);
+ }
+ if (tbl) free(tbl);
+ bh->txt = s.s;
+ bh->l_txt = 1 + s.l;