From 2ff207bd16bb3094843395450aa48936dd774ecb Mon Sep 17 00:00:00 2001
From: James Bonfield <jkb@sanger.ac.uk>
Date: Fri, 27 Sep 2024 16:11:07 +0100
Subject: [PATCH] Replace home-brew string end searching with memchr. (#1842)

With long aux tags the trival while loop can be suprisingly slow.

"while (s < end && *s) ++s;" isn't well vectorised or turned into
word-by-word processing by neither gcc nor clang, but these tricks are
used by the system memchr implementation.

An alternative could be this (used in my WIP VCF parser), which is
more optimised for relatively short strings.  Included here just for
potential future reference on systems with noddy memchr
implementations.

    #define haszero(x) (((x)-0x0101010101010101UL)&~(x)&0x8080808080808080UL)
    static inline char *memchr8(char *s, char sym, size_t len) {
        const uint64_t sym8 = sym * 0x0101010101010101UL;
        uint64_t *s8 = (uint64_t *)s;
        uint64_t *s8_end = (uint64_t *)(s+(len&~7));

        while (s8 < s8_end && !haszero(*s8 ^ sym8))
            s8++;

        // Precise identification
        char *s_end = s + len;
        s = (char *)s8;
        while (s < s_end && *s != sym) {
            s++;
        }

        return s < s_end ? s : NULL;
    }
---
 sam.c | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sam.c b/sam.c
index 7e58da6e7..3593b5507 100644
--- a/sam.c
+++ b/sam.c
@@ -4856,8 +4856,8 @@ static inline uint8_t *skip_aux(uint8_t *s, uint8_t *end)
     switch (size) {
     case 'Z':
     case 'H':
-        while (s < end && *s) ++s;
-        return s < end ? s + 1 : end;
+        s = memchr(s, 0, end-s);
+        return s ? s+1 : end;
     case 'B':
         if (end - s < 5) return NULL;
         size = aux_type2size(*s); ++s;