From 207a5e739794218635f9b5d0d4642b7447f2fcd8 Mon Sep 17 00:00:00 2001
From: Hasindu Gamaarachchi <hasindu2008@gmail.com>
Date: Mon, 9 Sep 2024 19:48:41 +1000
Subject: [PATCH] revert some changes

---
 src/eventalign.c | 80 ++++++++++++++++++++++++------------------------
 src/f5c.h        |  2 +-
 2 files changed, 41 insertions(+), 41 deletions(-)

diff --git a/src/eventalign.c b/src/eventalign.c
index 9978cedb..7b59471a 100644
--- a/src/eventalign.c
+++ b/src/eventalign.c
@@ -1263,32 +1263,32 @@ struct EventAlignmentParameters
 };
 
 
-static inline int32_t *get_ref_to_read_map(AlignedSegment& aligned_pairs, int32_t *ref_seg_len_ptr){
-
-    int32_t ref_start = aligned_pairs.front().ref_pos;
-    int32_t ref_end = aligned_pairs.back().ref_pos;
-    int32_t ref_seg_len = ref_end - ref_start + 1;
-    *ref_seg_len_ptr = ref_seg_len;
-    assert(ref_start < ref_end);
-    assert(ref_seg_len > 0);
-
-    int32_t *ref_to_read_map = (int32_t*)malloc(sizeof(int32_t)*ref_seg_len);
-    MALLOC_CHK(ref_to_read_map);
-    for(int32_t i=0; i<ref_seg_len; i++){
-        ref_to_read_map[i] = -1;
-    }
-    for(size_t i = 0; i < aligned_pairs.size(); i++){
-        int32_t ref_pos = aligned_pairs[i].ref_pos - ref_start;
-        int32_t read_pos = aligned_pairs[i].read_pos;
-        ref_to_read_map[ref_pos] = read_pos;
-    }
+// static inline int32_t *get_ref_to_read_map(AlignedSegment& aligned_pairs, int32_t *ref_seg_len_ptr){
+
+//     int32_t ref_start = aligned_pairs.front().ref_pos;
+//     int32_t ref_end = aligned_pairs.back().ref_pos;
+//     int32_t ref_seg_len = ref_end - ref_start + 1;
+//     *ref_seg_len_ptr = ref_seg_len;
+//     assert(ref_start < ref_end);
+//     assert(ref_seg_len > 0);
+
+//     int32_t *ref_to_read_map = (int32_t*)malloc(sizeof(int32_t)*ref_seg_len);
+//     MALLOC_CHK(ref_to_read_map);
+//     for(int32_t i=0; i<ref_seg_len; i++){
+//         ref_to_read_map[i] = -1;
+//     }
+//     for(size_t i = 0; i < aligned_pairs.size(); i++){
+//         int32_t ref_pos = aligned_pairs[i].ref_pos - ref_start;
+//         int32_t read_pos = aligned_pairs[i].read_pos;
+//         ref_to_read_map[ref_pos] = read_pos;
+//     }
 
-    // for(int32_t i=0; i<ref_seg_len; i++){
-    //     fprintf(stderr, "ref_to_read_map[%d] = %d\n",i+ref_start,ref_to_read_map[i]);
-    // }
+//     // for(int32_t i=0; i<ref_seg_len; i++){
+//     //     fprintf(stderr, "ref_to_read_map[%d] = %d\n",i+ref_start,ref_to_read_map[i]);
+//     // }
 
-    return ref_to_read_map;
-}
+//     return ref_to_read_map;
+// }
 
  std::vector<event_alignment_t> align_read_to_ref(const EventAlignmentParameters& params, char *ref)
 {
@@ -1346,8 +1346,8 @@ static inline int32_t *get_ref_to_read_map(AlignedSegment& aligned_pairs, int32_
 
         AlignedSegment& aligned_pairs = aligned_segments[segment_idx];
 
-        int32_t ref_seg_len = 0;
-        int32_t *ref_to_read_map = get_ref_to_read_map(aligned_pairs, &ref_seg_len);
+        //int32_t ref_seg_len = 0;
+        //int32_t *ref_to_read_map = get_ref_to_read_map(aligned_pairs, &ref_seg_len);
 
         if(params.region_start != -1 && params.region_end != -1) {
             //fprintf(stderr, "params.region_start = %d params.region_end = %d\n",params.region_start,params.region_end);
@@ -1498,8 +1498,8 @@ static inline int32_t *get_ref_to_read_map(AlignedSegment& aligned_pairs, int32_
                     ea.ref_position = curr_start_ref + as.kmer_idx;
                     std::string ref__kmer = ref_seq.substr(ea.ref_position - ref_offset, k);
                     kmer_cpy(ea.ref_kmer, ref__kmer.c_str(),k);
-                    assert(as.kmer_idx < ref_seg_len - params.kmer_size + 1);
-                    ea.read_position = ref_to_read_map[as.kmer_idx];
+                    //assert(as.kmer_idx < ref_seg_len - params.kmer_size + 1);
+                    //ea.read_position = ref_to_read_map[as.kmer_idx];
 
                     // event
                     ea.read_idx = params.read_idx;
@@ -1560,7 +1560,7 @@ static inline int32_t *get_ref_to_read_map(AlignedSegment& aligned_pairs, int32_
             tester_i++;
         } // for realignmentsegment
         // fprintf(stderr, "tester_i = %d\n",tester_i);
-        free(ref_to_read_map);
+        //free(ref_to_read_map);
     } // for bam aligned segment
     // fprintf(stderr, "alignment_output len = %d\n",alignment_output.size());
     // assert(alignment_output.size() == 4451);
@@ -2098,18 +2098,18 @@ std::vector<float> get_scaled_samples_for_event(const event_table* events,scalin
 // }
 
 
-static inline void sprintf_read_kmer(kstring_t *sp, int32_t read_pos, char *read, int32_t read_len, uint32_t kmer_size){
+// static inline void sprintf_read_kmer(kstring_t *sp, int32_t read_pos, char *read, int32_t read_len, uint32_t kmer_size){
 
-    if(read_pos == -1){
-        sprintf_append(sp, "\t.\t.");
-        return;
-    } else {
-        char kmer[kmer_size+1];
-        kmer_cpy(kmer, read+read_pos, kmer_size);
-        sprintf_append(sp, "\t%d\t%s", read_pos, kmer);
-    }
+//     if(read_pos == -1){
+//         sprintf_append(sp, "\t.\t.");
+//         return;
+//     } else {
+//         char kmer[kmer_size+1];
+//         kmer_cpy(kmer, read+read_pos, kmer_size);
+//         sprintf_append(sp, "\t%d\t%s", read_pos, kmer);
+//     }
 
-}
+// }
 
 char *emit_event_alignment_tsv(uint32_t strand_idx,
                               const event_table* et, model_t* model, uint32_t kmer_size, scalings_t scalings,
@@ -2245,7 +2245,7 @@ char *emit_event_alignment_tsv(uint32_t strand_idx,
             sample_str.resize(sample_str.size() - 1);
             sprintf_append(sp, "\t%s", sample_str.c_str());
         }
-        sprintf_read_kmer(sp, ea.read_position, read, read_len, kmer_size);
+        //sprintf_read_kmer(sp, ea.read_position, read, read_len, kmer_size);
         sprintf_append(sp, "\n");
     }
 
diff --git a/src/f5c.h b/src/f5c.h
index dca4bacd..c9b8a4a5 100644
--- a/src/f5c.h
+++ b/src/f5c.h
@@ -201,7 +201,7 @@ typedef struct {
     //int32_t strand_idx;
     int32_t event_idx;
     bool rc;
-    int32_t read_position;
+    //int32_t read_position;
 
     // hmm data
     char model_kmer[MAX_KMER_SIZE + 1];