Make a dynamic dispatcher function for nibble2base

samtools · Apr 2, 2024 · 06e6545 · 06e6545
1 parent 0840b8d
commit 06e6545
Showing 1 changed file with 45 additions and 18 deletions.
diff --git a/sam_internal.h b/sam_internal.h
@@ -25,10 +25,9 @@ DEALINGS IN THE SOFTWARE.  */
 
 #include <errno.h>
 #include <stdint.h>
+#include "htslib/hts_defs.h"
 #include "htslib/sam.h"
-#ifdef __SSSE3__
-#include "tmmintrin.h"
-#endif
+
 #ifdef __cplusplus
 extern "C" {
 #endif
@@ -70,7 +69,7 @@ static inline int possibly_expand_bam_data(bam1_t *b, size_t bytes) {
  * for (i = 0; i < len; i++)
  *    seq[i] = seq_nt16_str[bam_seqi(nib, i)];
  */
-static inline void nibble2base(uint8_t *nib, char *seq, int len) {
+static inline void nibble2base_default(uint8_t *nib, char *seq, int len) {
     static const char code2base[512] =
         "===A=C=M=G=R=S=V=T=W=Y=H=K=D=B=N"
         "A=AAACAMAGARASAVATAWAYAHAKADABAN"
@@ -89,12 +88,33 @@ static inline void nibble2base(uint8_t *nib, char *seq, int len) {
         "B=BABCBMBGBRBSBVBTBWBYBHBKBDBBBN"
         "N=NANCNMNGNRNSNVNTNWNYNHNKNDNBNN";
 
+    int i, len2 = len/2;
+    seq[0] = 0;
+
+    for (i = 0; i < len2; i++)
+        // Note size_t cast helps gcc optimiser.
+        memcpy(&seq[i*2], &code2base[(size_t)nib[i]*2], 2);
+
+    if ((i *= 2) < len)
+        seq[i] = seq_nt16_str[bam_seqi(nib, i)];
+}
+
+#if HTS_GCC_AT_LEAST(4,8)
+/*
+ * Convert a nibble encoded BAM sequence to a string of bases.
+ * 
+ * Using SSSE3 instructions, 16 codepoints that hold 2 bases each can be 
+ * unpacked into 32 indexes from 0-15. Using the pshufb instruction these can 
+ * be converted to the IUPAC characters. 
+ * It falls back on the nibble2base_default function for the remainder.
+ */
+#include "tmmintrin.h"
+__attribute__((target("ssse3")))
+static inline void nibble2base_ssse3(uint8_t *nib, char *seq, int len) {
     seq[0] = 0;
     const char *seq_end_ptr = seq + len;
     char *seq_cursor = seq;
-    const uint8_t *nibble_cursor = nib;
-    const char *seq_end_ptr_twoatatime = seq + (len & (~1ULL));
-    #ifdef __SSSE3__
+    uint8_t *nibble_cursor = nib;
     const char *seq_vec_end_ptr = seq_end_ptr - (2 * sizeof(__m128i));
     __m128i first_upper_shuffle = _mm_setr_epi8(
         0, 0xff, 1, 0xff, 2, 0xff, 3, 0xff, 4, 0xff, 5, 0xff, 6, 0xff, 7, 0xff);
@@ -141,21 +161,28 @@ static inline void nibble2base(uint8_t *nib, char *seq, int len) {
         nibble_cursor += sizeof(__m128i);
         seq_cursor += 2 * sizeof(__m128i);
     }
-    #endif
-    while (seq_cursor < seq_end_ptr_twoatatime) {
-        // Note size_t cast helps gcc optimiser.
-        memcpy(seq_cursor, code2base + ((size_t)*nibble_cursor * 2), 2);
-        seq_cursor += 2;
-        nibble_cursor += 1;
+    nibble2base_default(nibble_cursor, seq_cursor, seq_end_ptr - seq_cursor);
+}
+static void (*nibble2base)(uint8_t *nib, char *seq, int len);
+
+static void nibble2base_dispatch(uint8_t *nib, char *seq, int len) {
+    if (__builtin_cpu_supports("ssse3")) {
+        nibble2base = nibble2base_ssse3;
     }
-    if (seq_cursor != seq_end_ptr) {
-        /* There is a single encoded nuc left */
-        uint8_t nibble_c = *nibble_cursor;
-        uint8_t upper_nuc_index = nibble_c >> 4;
-        seq_cursor[0] = seq_nt16_str[upper_nuc_index];
+    else {
+        nibble2base = nibble2base_default;
     }
+
+    return nibble2base(nib, seq, len);
 }
 
+static void (*nibble2base)(uint8_t *nib, char *seq, int len) = nibble2base_dispatch;
+
+#else
+static inline void nibble2base(uint8_t *nib, char *seq, int len) {
+    return nibble2base_default(nib, seq, len);
+}
+#endif
 #ifdef __cplusplus
 }
 #endif