Guard AVX2 ksw2 declaration and calls behind #ifndef KSW_USE_ARM

The AVX2 object file is not compiled on ARM, so the declaration and
call sites must be guarded to avoid undefined symbol errors on aarch64.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: Rob Patro

include/ksw2pp/ksw2.h

@@ -58,8 +58,10 @@ void ksw_extz(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t
 
 void ksw_extz2_sse(/*unsigned int simd, */void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
 				   int8_t q, int8_t e, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez, int cutoff);
+#ifndef KSW_USE_ARM
 void ksw_extz2_avx2(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
            int8_t q, int8_t e, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez, int cutoff);
+#endif
 void ksw_extz2_sse41(/*unsigned int simd, */void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
            int8_t q, int8_t e, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez, int cutoff);
 void ksw_extz2_sse2(/*unsigned int simd, */void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,

src/ksw2pp/KSW2Aligner.cpp

@@ -249,11 +249,14 @@ int KSW2Aligner::operator()(const char* const queryOriginal,
   int max_qt_len = (queryLength > targetLength) ? queryLength : targetLength;
   int w = (config_.bandwidth > max_qt_len) ? max_qt_len : config_.bandwidth;
   int z = config_.dropoff;
+  #ifndef KSW_USE_ARM
   if (haveAVX2) {
     ksw_extz2_avx2(kalloc_allocator_.get(), qlen, query_.data(), tlen,
                 target_.data(), config_.alphabetSize, mat_.data(), q, e, w, z,
                 config_.end_bonus, config_.flag, ez, cutoff);
-  } else if (haveSSE41) {
+  } else
+  #endif
+  if (haveSSE41) {
     ksw_extz2_sse41(kalloc_allocator_.get(), qlen, query_.data(), tlen,
                 target_.data(), config_.alphabetSize, mat_.data(), q, e, w, z,
                 config_.end_bonus, config_.flag, ez, cutoff);
@@ -398,11 +401,14 @@ int KSW2Aligner::operator()(const uint8_t* const query_, const int queryLength,
   int max_qt_len = (queryLength > targetLength) ? queryLength : targetLength;
   int w = (config_.bandwidth > max_qt_len) ? max_qt_len : config_.bandwidth;
   int z = config_.dropoff;
+  #ifndef KSW_USE_ARM
   if (haveAVX2) {
     ksw_extz2_avx2(kalloc_allocator_.get(), qlen, query_, tlen, target_,
                 config_.alphabetSize, mat_.data(), q, e, w, z, config_.end_bonus, config_.flag,
                 ez, cutoff);
-  } else if (haveSSE41) {
+  } else
+  #endif
+  if (haveSSE41) {
     ksw_extz2_sse41(kalloc_allocator_.get(), qlen, query_, tlen, target_,
                 config_.alphabetSize, mat_.data(), q, e, w, z, config_.end_bonus, config_.flag,
                 ez, cutoff);