Small fixes

.gitignore

@@ -1,2 +1,7 @@
 **/out
+**/dpu-out
 **/build
+.vscode/*
+Datasets/const-seq/*
+Datasets/var-seq/*
+Datasets/bin/*

Datasets/generatedata.sh

@@ -0,0 +1,17 @@
+#! /usr/bin/bash 
+
+# make sure Datasets/bin/generate_dataset exists (https://github.com/smarco/WFA)
+
+set -x
+
+seqLengths=("100" "1000" "5000" "10000" "20000" "25000" "50000" "100000")
+
+for seqLength in ${seqLengths[@]}; do
+    ./bin/generate_dataset --n 100000 -l $seqLength --e 0.01 --o ./const-seq/seq-l$seqLength-e1-100KPairs
+done
+
+for seqLength in ${seqLengths[@]}; do
+    ./bin/generate_dataset --n 100000 -l $seqLength --e 0.05 --o ./const-seq/seq-l$seqLength-e5-100KPairs
+done
+
+echo "finished generating data"

WFA/DPU-MRAM/dpu/wfa.c

@@ -140,16 +140,22 @@ void affine_wfa_reduce_wvs(wfa_component *wfa, awf_offset_t pattern_length, awf_
     }
 }
 // insert new score
+// change this function so it allocates using score % needed
+// EDIT THIS FUNCTION!!!!
 wfa_component *allocate_new_score(dpu_alloc_wram_t *allocator, int score, int lo, int hi, int kernel, uint32_t *mramIdx, dpu_alloc_mram_t *dpu_alloc_mram)
 {
     int wv_len = hi - lo + 1;
     uint32_t cmpnt_size = 0;
 
+// these two lines show that the size of the wfa_cmpnt is constant, but the size of the wfa cmpnt's offsets is not constant.
     wfa_component *wfa_cmpnt = (wfa_component *)allocate_new(allocator, sizeof(wfa_component));
     awf_offset_t *offset_ptr = (awf_offset_t *)allocate_new(allocator, (wv_len * sizeof(awf_offset_t)));
 
     wfa_cmpnt->mwavefront = (awf_offset_t *)(offset_ptr - lo);
     cmpnt_size += ROUND_UP_MULTIPLE_8(wv_len * sizeof(awf_offset_t));
+    // kernel = 3 means I and D
+    // kernel = 2 means I
+    // kernel = 1 means D
     if (kernel == 3 || kernel == 1)
     {
 
@@ -281,6 +287,7 @@ wfa_component *affine_wfa_compute_next(int score, uint32_t *mramIdx, dpu_alloc_w
     int o_score = score - GAP_O - GAP_E;
     int e_score = score - GAP_E;
 
+// edit here so it computes differently and loads mwaefront from score % something
     wfa_component *wfa_mismatch = (mismatch_score < 0 || mramIdx[mismatch_score] == 0) ? NULL : load_mwavefront_cmpnt_from_mram(alloc_obj, mramIdx[mismatch_score]);
     wfa_component *wfa_o_score = (o_score < 0 || mramIdx[o_score] == 0) ? NULL : load_mwavefront_cmpnt_from_mram(alloc_obj, mramIdx[o_score]);
     wfa_component *wfa_e_score = (e_score < 0 || mramIdx[e_score] == 0) ? NULL : load_idwavefront_cmpnt_from_mram(alloc_obj, mramIdx[e_score]);

WFA/DPU-MRAM/host/host.c

@@ -338,13 +338,13 @@ int main(int argc, char *argv[])
         for (i = 0; i < dpuParams[dpu].dpuNumReads; ++i)
         {
             fprintf(output_file, "%d, %d, \n", dpuResults[dpu][i].idx, dpuResults[dpu][i].score);
+
+#ifdef BACKTRACE
             edit_cigar_t cigar;
             cigar.score = dpuResults[dpu][i].score;
             cigar.max_operations = dpuResults[dpu][i].max_operations;
             cigar.begin_offset = dpuResults[dpu][i].begin_offset;
             cigar.end_offset = dpuResults[dpu][i].end_offset;
-
-#ifdef BACKTRACE
             cigar.operations = (char *)malloc(ROUND_UP_MULTIPLE_8(cigar.max_operations));
             strncpy(cigar.operations, &(operations[i * 2 * READ_SIZE]), ROUND_UP_MULTIPLE_8(cigar.max_operations));
             edit_cigar_print(&cigar, output_file);