From 0aef2810c879f03a379e66aab43e52ec9ec1f9bf Mon Sep 17 00:00:00 2001
From: Christoffer Lerno <christoffer@aegik.com>
Date: Fri, 10 Sep 2021 19:27:42 +0200
Subject: [PATCH] Added fasta example.

---
 resources/examples/fasta.c3 | 105 ++++++++++++++++++++++++++++++++++++
 src/compiler/llvm_codegen.c |   4 ++
 src/compiler/sema_expr.c    |   6 +--
 3 files changed, 112 insertions(+), 3 deletions(-)
 create mode 100644 resources/examples/fasta.c3

diff --git a/resources/examples/fasta.c3 b/resources/examples/fasta.c3
new file mode 100644
index 000000000..7cc25de49
--- /dev/null
+++ b/resources/examples/fasta.c3
@@ -0,0 +1,105 @@
+module fasta;
+
+const IM = 139968;
+const IA = 3877;
+const IC = 29573;
+const SEED = 42;
+
+uint seed = SEED;
+
+func float fasta_rand(float max)
+{
+    seed = (seed * IA + IC) % IM;
+    return max * seed / IM;
+}
+
+private char[] alu =
+  "GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGG"
+  "GAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGA"
+  "CCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAAT"
+  "ACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCA"
+  "GCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGG"
+  "AGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCC"
+  "AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA";
+
+extern func int atoi(char *s);
+extern func int printf(char *s, ...);
+extern func void putchar(int c);
+
+char[] iub = "acgtBDHKMNRSVWY";
+double[*] iub_p = {
+  0.27,
+  0.12,
+  0.12,
+  0.27,
+  0.02,
+  0.02,
+  0.02,
+  0.02,
+  0.02,
+  0.02,
+  0.02,
+  0.02,
+  0.02,
+  0.02,
+  0.02 };
+
+char[] homosapiens = "acgt";
+double[*] homosapiens_p = {
+  0.3029549426680,
+  0.1979883004921,
+  0.1975473066391,
+  0.3015094502008
+};
+
+const LINELEN = 60;
+
+// slowest character-at-a-time output
+func void repeat_fasta(char[] seq, int n)
+{
+    usize len = seq.len();
+    int i = void;
+    for (i = 0; i < n; i++)
+    {
+        putchar(seq[i % len]);
+        if (i % LINELEN == LINELEN - 1) putchar('\n');
+    }
+    if (i % LINELEN != 0) putchar('\n');
+}
+
+func void random_fasta(char[] symb, double[] probability, int n)
+{
+    assert(symb.len() == probability.len());
+    int len = (int)(probability.len());
+    int i = void;
+    for (i = 0; i < n; i++)
+    {
+        double v = fasta_rand(1.0);
+        /* slowest idiomatic linear lookup.  Fast if len is short though. */
+        int j = void;
+        for (j = 0; j < len - 1; j++)
+        {
+            v -= probability[j];
+            if (v < 0) break;
+        }
+        putchar(symb[j]);
+        if (i % LINELEN == LINELEN - 1) putchar('\n');
+    }
+    if (i % LINELEN != 0) putchar('\n');
+}
+
+func void main(int argc, char **argv)
+{
+    int n=1000;
+    if (argc > 1) n = atoi(argv[1]);
+
+    printf(">ONE Homo sapiens alu\n");
+    repeat_fasta(alu, n * 2);
+
+    printf(">TWO IUB ambiguity codes\n");
+    random_fasta(iub, &iub_p, n * 3);
+
+    printf(">THREE Homo sapiens frequency\n");
+    random_fasta(homosapiens, &homosapiens_p, n * 5);
+
+}
diff --git a/src/compiler/llvm_codegen.c b/src/compiler/llvm_codegen.c
index f4de9f089..30fabbe9e 100644
--- a/src/compiler/llvm_codegen.c
+++ b/src/compiler/llvm_codegen.c
@@ -94,6 +94,10 @@ LLVMValueRef llvm_emit_const_initializer(GenContext *c, ConstInitializer *const_
 			LLVMTypeRef element_type_llvm = llvm_get_type(c, element_type);
 			ConstInitializer **elements = const_init->init_array_full;
 			ArrayIndex size = array_type->array.len;
+			if (array_type->type_kind == TYPE_SUBARRAY)
+			{
+				size = vec_size(elements);
+			}
 			assert(size > 0);
 			LLVMValueRef *parts = VECNEW(LLVMValueRef, size);
 			for (ArrayIndex i = 0; i < size; i++)
diff --git a/src/compiler/sema_expr.c b/src/compiler/sema_expr.c
index 2a4d137ba..4b1ba57e4 100644
--- a/src/compiler/sema_expr.c
+++ b/src/compiler/sema_expr.c
@@ -3096,18 +3096,18 @@ static inline bool sema_expr_analyse_array_plain_initializer(Context *context, T
 		ConstInitializer *const_init = CALLOCS(ConstInitializer);
 		const_init->kind = CONST_INIT_ARRAY_FULL;
 		const_init->type = type_flatten(initializer->type);
-		ConstInitializer **inits = MALLOC(sizeof(ConstInitializer *) * vec_size(elements));
+		ConstInitializer **inits = VECNEW(ConstInitializer*, vec_size(elements));
 		VECEACH(elements, i)
 		{
 			Expr *expr = elements[i];
 			if (expr->expr_kind == EXPR_CONST && expr->const_expr.const_kind == CONST_LIST)
 			{
-				inits[i] = expr->const_expr.list;
+				vec_add(inits, expr->const_expr.list);
 				continue;
 			}
 			ConstInitializer *element_init = MALLOC(sizeof(ConstInitializer));
 			sema_create_const_initializer_value(element_init, expr);
-			inits[i] = element_init;
+			vec_add(inits, element_init);
 		}
 		const_init->init_array_full = inits;
 		expr_set_as_const_list(initializer, const_init);