Bug fix to finding best exit point on last row.

jkbonfield · jkbonfield · commit b6af267ec9d7 · 2017-10-25T15:18:12.000+01:00
diff --git a/ksw.c b/ksw.c
@@ -616,11 +616,11 @@ int ksw_global_end(int qlen, const uint8_t *query, int tlen, const uint8_t *targ
 		for (j = beg; j <= qlen; j++) {
 			if (score < eh[j].h) {
 				score = eh[j].h;
-				if (j < k && n_cigar_ && cigar_)
-					cigar = push_cigar(&n_cigar, &m_cigar, cigar, 1, k-j);
 				k = j;
 			}
 		}
+		if (k < qlen-1 && n_cigar_ && cigar_)
+		    cigar = push_cigar(&n_cigar, &m_cigar, cigar, 1, qlen - k -1);
 	}
 	if (n_cigar_ && cigar_) { // backtrack
 		int which = 0;

Original file line number	Diff line number	Diff line change
`@@ -616,11 +616,11 @@ int ksw_global_end(int qlen, const uint8_t query, int tlen, const uint8_t targ`
`616`	`616`	`for (j = beg; j <= qlen; j++) {`
`617`	`617`	`if (score < eh[j].h) {`
`618`	`618`	`score = eh[j].h;`
`619`		`- if (j < k && n_cigar_ && cigar_)`
`620`		`- cigar = push_cigar(&n_cigar, &m_cigar, cigar, 1, k-j);`
`621`	`619`	`k = j;`
`622`	`620`	`}`
`623`	`621`	`}`
	`622`	`+ if (k < qlen-1 && n_cigar_ && cigar_)`
	`623`	`+ cigar = push_cigar(&n_cigar, &m_cigar, cigar, 1, qlen - k -1);`
`624`	`624`	`}`
`625`	`625`	`if (n_cigar_ && cigar_) { // backtrack`
`626`	`626`	`int which = 0;`