Add an hts_crc32 function to use zlib or libdeflate. (#1850)

This follows on from the hts_md5* functions which wrap up either
OpenSSL or our own implementation.  Libdeflate's crc32 function is
considerably faster than the native zlib, so we want to use it in (for
example) the new "samtools checksum" code, but we do not wish to add
baggage of looking for libdeflate in the configure script.

Author: jkbonfield

bgzf.c

@@ -548,6 +548,10 @@ BGZF *bgzf_hopen(hFILE *hfp, const char *mode)
 }
 
 #ifdef HAVE_LIBDEFLATE
+uint32_t hts_crc32(uint32_t crc, const void *buf, size_t len) {
+    return libdeflate_crc32(crc, buf, len);
+}
+
 int bgzf_compress(void *_dst, size_t *dlen, const void *src, size_t slen, int level)
 {
     if (slen == 0) {
@@ -607,6 +611,10 @@ int bgzf_compress(void *_dst, size_t *dlen, const void *src, size_t slen, int le
 
 #else
 
+uint32_t hts_crc32(uint32_t crc, const void *buf, size_t len) {
+    return crc32(crc, buf, len);
+}
+
 int bgzf_compress(void *_dst, size_t *dlen, const void *src, size_t slen, int level)
 {
     uint32_t crc;
@@ -1350,13 +1358,7 @@ static void *bgzf_encode_level0_func(void *arg) {
     u16_to_le(~j->uncomp_len, j->comp_data + BLOCK_HEADER_LENGTH + 3);
 
     // Trailer (CRC, uncompressed length)
-#ifdef HAVE_LIBDEFLATE
-    crc = libdeflate_crc32(0, j->comp_data + BLOCK_HEADER_LENGTH + 5,
-                           j->uncomp_len);
-#else
-    crc = crc32(crc32(0L, NULL, 0L),
-                (Bytef*)j->comp_data + BLOCK_HEADER_LENGTH + 5, j->uncomp_len);
-#endif
+    crc = hts_crc32(0, j->comp_data + BLOCK_HEADER_LENGTH + 5, j->uncomp_len);
     u32_to_le(crc, j->comp_data +  j->comp_len - 8);
     u32_to_le(j->uncomp_len, j->comp_data + j->comp_len - 4);
 

htslib/hts.h

@@ -1518,6 +1518,14 @@ static inline int hts_bin_level(int bin) {
     return l;
 }
 
+/**************************************
+ * Exposing the CRC32 implementation  *
+ * Either from zlib or libdeflate.    *
+ *************************************/
+HTSLIB_EXPORT
+uint32_t hts_crc32(uint32_t crc, const void *buf, size_t len);
+
+
 //! Compute the corresponding entry into the linear index of a given bin from
 //! a binning index
 /*!