Speed-up FASTA parsing in kseq.h with memchr (#756)

Co-authored-by: Valentyn Bezshapkin <walentyn.bzsz@gmail.com> Co-authored-by: Fabian Klötzl <fabian@kloetzl.info>
soedinglab · Oct 31, 2023 · 98406dd · 98406dd
1 parent dd6c017
commit 98406dd
Showing 1 changed file with 4 additions and 3 deletions.
diff --git a/lib/ksw2/kseq.h b/lib/ksw2/kseq.h
@@ -113,9 +113,10 @@ typedef struct __kstring_t {
 					if (ks->end == -1) { ks->is_eof = 1; return -3; }	\
 				} else break;											\
 			}															\
-			if (delimiter == KS_SEP_LINE) { \
-				for (i = ks->begin; i < ks->end; ++i) \
-					if (ks->buf[i] == '\n') { ks->newline+=(append == 1); break; } \
+			if (delimiter == KS_SEP_LINE) { 							\
+				unsigned char *sep = (unsigned char*)memchr(ks->buf + ks->begin, '\n', ks->end - ks->begin); \
+    			i = sep != NULL ? sep - (unsigned char*)ks->buf : ks->end; \
+    			ks->newline += (sep != NULL && append == 1); 				\
 			} else if (delimiter > KS_SEP_MAX) {						\
 				for (i = ks->begin; i < ks->end; ++i)					\
 					if (ks->buf[i] == delimiter) break;					\