Backport htslib/kseq.h parsing performance improvement (PR #1227)

Apply the main part of PR samtools/htslib#1674. Pysam does use kseq itself, so it is worth applying this now without waiting for the next HTSlib release to be imported. Co-Authored-By: Fabian Klötzl <[email protected]>
pysam-developers · Sep 28, 2023 · 7d1df29 · 7d1df29
1 parent adf52b9
commit 7d1df29
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/htslib/htslib/kseq.h b/htslib/htslib/kseq.h
@@ -110,8 +110,8 @@
 				} else break; \
 			} \
 			if (delimiter == KS_SEP_LINE) {  \
-				for (i = ks->begin; i < ks->end; ++i)  \
-					if (ks->buf[i] == '\n') break; \
+				unsigned char *sep = memchr(ks->buf + ks->begin, '\n', ks->end - ks->begin); \
+				i = sep != NULL ? sep - ks->buf : ks->end; \
 			} else if (delimiter > KS_SEP_MAX) { \
 				for (i = ks->begin; i < ks->end; ++i) \
 					if (ks->buf[i] == delimiter) break; \