r244: fixed extra aa and a potential memory bug

Resolves #47
lh3 · Mar 6, 2024 · af102cf · af102cf
1 parent 61a352f
commit af102cf
Show file tree

Hide file tree

Showing 3 changed files with 4 additions and 2 deletions.
diff --git a/format.c b/format.c
@@ -277,7 +277,7 @@ static void mp_write_residue(kstring_t *out, const mp_idx_t *mi, const mp_mapopt
 		}
 	}
 	assert(nl == r->ve - r->vs);
-	if (l_nt == r->ve - r->vs + 3) { // then print one more codon
+	if (l_nt == r->ve - r->vs + 3 && str[4][w4-1] != '*') { // then print one more codon
 		uint8_t n1 = nt[nl], n2 = nt[nl + 1], n3 = nt[nl + 2], nt_aa, codon;
 		codon = n1<<4 | n2<<2 | n3;
 		nt_aa = n1 > 3 || n2 > 3 || n3 > 3? ns_tab_aa20['X'] : ns_tab_codon[codon];

diff --git a/miniprot.h b/miniprot.h
@@ -3,7 +3,7 @@
 
 #include <stdint.h>
 
-#define MP_VERSION "0.12-r243-dirty"
+#define MP_VERSION "0.12-r244-dirty"
 
 #define MP_F_NO_SPLICE    0x1
 #define MP_F_NO_ALIGN     0x2

diff --git a/ntseq.c b/ntseq.c
@@ -101,6 +101,8 @@ int64_t mp_ntseq_get(const mp_ntdb_t *db, int32_t cid, int64_t st, int64_t en, i
 int64_t mp_ntseq_get_by_v(const mp_ntdb_t *nt, int32_t vid, int64_t st, int64_t en, uint8_t *seq)
 {
 	int64_t ctg_len = nt->ctg[vid>>1].len;
+	if (st < 0 || en < 0 || st >= ctg_len) return -1;
+	en = en <= ctg_len? en : ctg_len;
 	return mp_ntseq_get(nt, vid>>1, vid&1? ctg_len - en : st, vid&1? ctg_len - st : en, vid&1, seq);
 }