Merge pull request #156 from hiruna72/paf_fix

add assertion to count signal samples and fix wrong insertion at the begnning of ss string

src/resquiggle.c

@@ -339,6 +339,7 @@ void output_db_rsq(core_t* core, db_t* db, int8_t fmt) {
  int8_t ff = 1; //first start flag
  int matches = 0;
  int8_t rna = core->opt.flag & F5C_RNA;
+ int64_t count_samples = 0;
 
  if (rna){
  for (int j = 0; j < n_kmers/2; ++j) {
@@ -372,6 +373,7 @@ void output_db_rsq(core_t* core, db_t* db, int8_t fmt) {
  if(ff) {
  signal_start_point2 = signal_start_point;
  read_start = j;
+ ci = signal_start_point;
  ff=0;
  }
  signal_end_point2=signal_end_point = et.event[end_event_idx].start + (int)et.event[end_event_idx].length; //non-inclusive
@@ -383,12 +385,16 @@ void output_db_rsq(core_t* core, db_t* db, int8_t fmt) {
  }
  if(j==0) ci = signal_start_point;
  ci += (mi = signal_start_point - ci);
- if(mi) sprintf_append(sp,"%dI",(int)mi);
+ if(mi) {
+ sprintf_append(sp, "%dI", (int)mi);
+ count_samples += mi;
+ }
  ci += (mi = signal_end_point-signal_start_point);
 
  if(mi) {
  matches++;
  sprintf_append(sp,"%d,",(int)mi);
+ count_samples += mi;
  }
  }
 
@@ -420,7 +426,7 @@ void output_db_rsq(core_t* core, db_t* db, int8_t fmt) {
  }
 
  if(fmt==1){
-
+ assert(count_samples==(signal_end_point2-signal_start_point2));
  assert(n_kmers>0);
  str.s[str.l] = '\0';