Merge Martin's version 25/05/23 (#6)

Merge changes to core miraculix by Martin
alexfreudenberg · May 26, 2023 · 0c86c56 · 0c86c56
1 parent 24afe74
commit 0c86c56
Show file tree

Hide file tree

Showing 38 changed files with 2,802 additions and 834 deletions.
diff --git a/.gitignore b/.gitignore
@@ -13,6 +13,8 @@
 *.freq
 *.bed
 *.mem
+*.*~
+
 
 *.optrpt
 *.tgz
diff --git a/src/miraculix/1bit128.cc~ b/src/miraculix/1bit128.cc~
diff --git a/src/miraculix/2bitUint.cc b/src/miraculix/2bitUint.cc
@@ -305,7 +305,7 @@ if (gV) vD = variant < 256 ? genoVector2_double : genoVector2v256_double;
 sparseTGeno_header(2Bit) {
   BUG;
   // unsinns aufruf!!:
-   sparseTGenoOrigPlink(code, nrow_code, ncol_code,
+   sparseTGenoPlink(code, nrow_code, ncol_code,
 		    ldaInByte, coding,
 		    valueB, nIdx, rowIdxB, colIdxB, tSparse,
 		    global, utils, 

diff --git a/src/miraculix/3bitUint.cc b/src/miraculix/3bitUint.cc
@@ -56,8 +56,8 @@ void initiate_tableI(table_type **table, int tableSize,
 
   int d;
   int *nx = (int *) CALLOC(codesPerPartUnit, sizeof(int));
-
   *table = (table_type*) CALLOC(tableSize, sizeof(table_type));
+
   table_type* pt = *table;
 
   while (true) {

diff --git a/src/miraculix/5codes512.cc b/src/miraculix/5codes512.cc
@@ -32,10 +32,10 @@
 #include "5codes.h"
 
 
-#if defined AVX2    
+#if defined AVX512
 
 
-ASSERT_SIMD(5codes512, avx2);
+ASSERT_SIMD(5codes512, avx512f);
 
 #include "MX.h"
 #include "haplogeno.h" 
@@ -47,13 +47,13 @@ ASSERT_SIMD(5codes512, avx2);
 
 #else
 #include "avx_miss.h"
-  
+
 
 gV5_header(512, floatD, LongDouble, float, double) Sv
 gV5_header(512, double, LongDouble, double, double) Sv
 
 
-SIMD_MISS(5codes512, avx2);
+SIMD_MISS(5codes512, avx512f);
 
 #endif  // defined AVX
 // trafo2Geno1Geno128

diff --git a/src/miraculix/5codesAPI.c b/src/miraculix/5codesAPI.c
@@ -86,7 +86,7 @@ void plink2compressed(char *plink,
 
   // setOptions_compressed(0, 6, 0, 0, 0, 0, 0, 0, 1);
 
-   int nbytes = indiv /4;   printf("p2c snps=%d indiv=%d max_n=%d bytes/indiv=%d\n", snps, indiv, max_n, nbytes);
+   int nbytes = indiv /4;   //printf("p2c snps=%d indiv=%d max_n=%d bytes/indiv=%d\n", snps, indiv, max_n, nbytes);
   // exit(99);
  //  printf("c byte 1:5 = %d %d %d %d %d\n", *plink, *(plink+1), *(plink+2), *(plink+3), *(plink+4));
 
@@ -147,10 +147,10 @@ void sparse_times_plink(char *transsparse,// N: matrix as is (sparse row format)
 
   if (is(transcompressed)) {
     int tmp = snps; snps=indiv; indiv=tmp;
-    plink_transposed = plink;
+    plink = plink_transposed;
   }
 
-  sparseTGenoPlinkApi(plink_transposed, snps, indiv,
+  sparseTGenoPlinkApi(plink, indiv, snps, 
 		      B, nIdx, rowIdxB, colIdxB, is(transsparse), C, Ldc);
 
   return;
-Original file line number
+Diff line change
@@ Expand Up / @@ -13,6 +13,8 @@ @@
     *.freq
     *.bed
     *.mem
+    *.*~
     *.optrpt
     *.tgz