r236: output the number of in-frame stop codons

lh3 · Jun 24, 2023 · e9aa3a4 · e9aa3a4
1 parent 73c6691
commit e9aa3a4
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Showing 3 changed files with 5 additions and 2 deletions.
diff --git a/format.c b/format.c
@@ -310,7 +310,8 @@ void mp_write_paf(kstring_t *s, const mp_idx_t *mi, const mp_bseq1_t *seq, const
 	else mp_sprintf_lite(s, "%d\t%d\t", (int)r->vs, (int)r->ve);
 	if (r->p) {
 		int32_t k;
-		mp_sprintf_lite(s, "%d\t%d\t0\tAS:i:%d\tms:i:%d\tnp:i:%d\tda:i:%d\tdo:i:%d\t", r->p->n_iden * 3, r->p->blen, r->p->dp_score, r->p->dp_max, r->p->n_plus, r->p->dist_start, r->p->dist_stop);
+		mp_sprintf_lite(s, "%d\t%d\t0\tAS:i:%d\tms:i:%d\tnp:i:%d\tfs:i:%d\tst:i:%d\tda:i:%d\tdo:i:%d\t",
+			r->p->n_iden * 3, r->p->blen, r->p->dp_score, r->p->dp_max, r->p->n_plus, r->p->n_fs, r->p->n_stop, r->p->dist_start, r->p->dist_stop);
 		mp_sprintf_lite(s, "cg:Z:");
 		for (k = 0; k < r->p->n_cigar; ++k)
 			mp_sprintf_lite(s, "%d%c", r->p->cigar[k]>>4, NS_CIGAR_STR[r->p->cigar[k]&0xf]);

diff --git a/miniprot.1 b/miniprot.1
@@ -268,6 +268,8 @@ _
 AS	i	Alignment score from dynamic programming
 ms	i	Alignment score excluding introns
 np	i	Number of amino acid matches with positive scores
+fs	i	Number of frameshifts
+st	i	Number of in-frame stop codons
 da	i	Distance to the nearest start codon
 do	i	Distance to the nearest stop codon
 cg	Z	Protein CIGAR

diff --git a/miniprot.h b/miniprot.h
@@ -3,7 +3,7 @@
 
 #include <stdint.h>
 
-#define MP_VERSION "0.11-r235-dirty"
+#define MP_VERSION "0.11-r236-dirty"
 
 #define MP_F_NO_SPLICE    0x1
 #define MP_F_NO_ALIGN     0x2