Windows compatibility changes:

windows doesn't like uint32_t so changed to uint windows doesn't like casting ulong to uint (unsure why it was casting anyway. maybe 32 bit build?) moved some compatibilty code from dhtslib.htslib.sam.d to dhtslib.htslib.hts.d where it belongs Now unittests compile (DMD and LDC) so I assume most code compiles on windows closes #38 for now
blachlylab · Aug 12, 2020 · d5b24b9 · d5b24b9
1 parent a4c8f86
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diff --git a/source/dhtslib/htslib/hts.d b/source/dhtslib/htslib/hts.d
@@ -335,18 +335,42 @@ The input character may be either an IUPAC ambiguity code, '=' for 0, or
 '0'/'1'/'2'/'3' for a result of 1/2/4/8.  The result is encoded as 1/2/4/8
 for A/C/G/T or combinations of these bits for ambiguous bases.
 */
-extern const(char)[256] seq_nt16_table;
+
+version(Windows){
+    const (char)[256] seq_nt16_table = [
+        15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+        15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+        15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+        1, 2, 4, 8, 15,15,15,15, 15,15,15,15, 15, 0 /*=*/,15,15,
+        15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15,
+        15,15, 5, 6,  8,15, 7, 9, 15,10,15,15, 15,15,15,15,
+        15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15,
+        15,15, 5, 6,  8,15, 7, 9, 15,10,15,15, 15,15,15,15,
+
+        15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+        15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+        15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+        15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+        15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+        15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+        15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+        15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15
+    ];
+}else{
+    extern const(char)[256] seq_nt16_table;
+}
 
 /**! @abstract Table for converting a 4-bit encoded nucleotide to an IUPAC
 ambiguity code letter (or '=' when given 0).
 */
-extern __gshared const(char)[16] seq_nt16_str;
 
+version(Windows) __gshared const (char)[16] seq_nt16_str = ['=','A','C','M','G','R','S','V','T','W','Y','H','K','D','B','N'];
+else extern __gshared const(char)[16] seq_nt16_str;
 /**! @abstract Table for converting a 4-bit encoded nucleotide to about 2 bits.
 Returns 0/1/2/3 for 1/2/4/8 (i.e., A/C/G/T), or 4 otherwise (0 or ambiguous).
 */
-extern const int[] seq_nt16_int;
-
+version(Windows) const (int)[16] seq_nt16_int = [ 4, 0, 1, 4, 2, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4 ];
+else extern const int[] seq_nt16_int;
 /**!
   @abstract  Get the htslib version number
   @return    For released versions, a string like "N.N[.N]"; or git describe

diff --git a/source/dhtslib/htslib/sam.d b/source/dhtslib/htslib/sam.d
@@ -66,33 +66,6 @@ import dhtslib.htslib.kstring: __kstring_t, kstring_t;
 /// Highest SAM format version supported by this library
 auto SAM_FORMAT_VERSION = "1.6"c;
 
-// For whatever reason, these are neccessary on windows builds
-version(Windows){
-    const ubyte[256] seq_nt16_table = [
-        15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
-        15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
-        15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
-        1, 2, 4, 8, 15,15,15,15, 15,15,15,15, 15, 0 /*=*/,15,15,
-        15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15,
-        15,15, 5, 6,  8,15, 7, 9, 15,10,15,15, 15,15,15,15,
-        15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15,
-        15,15, 5, 6,  8,15, 7, 9, 15,10,15,15, 15,15,15,15,
-
-        15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
-        15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
-        15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
-        15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
-        15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
-        15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
-        15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
-        15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15
-    ];
-
-    const char[16] seq_nt16_str = ['=','A','C','M','G','R','S','V','T','W','Y','H','K','D','B','N'];
-
-    const int[16] seq_nt16_int = [ 4, 0, 1, 4, 2, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4 ];
-}
-
 /**********************
  *** SAM/BAM header ***
  **********************/

diff --git a/source/dhtslib/htslib/vcf.d b/source/dhtslib/htslib/vcf.d
@@ -248,12 +248,12 @@ struct bcf1_t { // @suppress(dscanner.style.phobos_naming_convention)
     float qual;   /// QUAL
 
     mixin(bitfields!(
-        uint32_t, "n_info", 16,
-        uint32_t, "n_allele", 16));
+        uint, "n_info", 16,     /// For whatever reason, windows doesn't like uint32_t
+        uint, "n_allele", 16));
 
     mixin(bitfields!(
-        uint32_t, "n_fmt", 8,
-        uint32_t, "n_sample", 24));
+        uint, "n_fmt", 8,       /// For whatever reason, windows doesn't like uint32_t
+        uint, "n_sample", 24));
 
     kstring_t _shared;      /// ??? (name mangled due to D reserved keyword shared)
     kstring_t indiv;        /// ???

diff --git a/source/dhtslib/sam.d b/source/dhtslib/sam.d
@@ -1031,7 +1031,7 @@ private char* reverse(char* str)
 {
     import core.stdc.string : strlen;
 
-    ulong i = strlen(str) - 1, j = 0;
+    auto i = strlen(str) - 1, j = 0;
     char ch;
     while (i > j)
     {