fix: correct BED coordinate system calculation (#103)

BED format uses 0-based, half-open intervals [start, end).
Changed length calculation from `end - start + 1` to `end - start`.

Files fixed:
- regions_bed.c: length calculation and validation warning
- dwgsim.c: 3 occurrences of region length calculation

Closes #102

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>

Author: nh13

src/dwgsim.c

@@ -498,7 +498,7 @@ void dwgsim_core(dwgsim_opt_t * opt)
       // recalculate the total length
       tot_len = 0;
       for(i=0;i<regions_bed->n;i++) {
-          tot_len += regions_bed->end[i] - regions_bed->start[i] + 1;
+          tot_len += regions_bed->end[i] - regions_bed->start[i];  // BED half-open
       }
   }
   if(NULL != contigs) {
@@ -538,7 +538,7 @@ void dwgsim_core(dwgsim_opt_t * opt)
                   m = 0;
                   for(i=0;i<regions_bed->n;i++) {
                       if(contig_i == regions_bed->contig[i]) {
-                          m += regions_bed->end[i] - regions_bed->start[i] + 1;
+                          m += regions_bed->end[i] - regions_bed->start[i];  // BED half-open
                       }
                   }
                   if(0 == m) {
@@ -692,7 +692,7 @@ void dwgsim_core(dwgsim_opt_t * opt)
                           // convert in the bed file
                           for(i=0;i<regions_bed->n;i++) { // TODO: regions are in sorted order... so optimize
                               if(contig_i == regions_bed->contig[i]) {
-                                  j = regions_bed->end[i] - regions_bed->start[i] + 1;
+                                  j = regions_bed->end[i] - regions_bed->start[i];  // BED half-open
                                   if(pos < j) {
                                       pos = regions_bed->start[i] + pos - 1; // zero-based
                                       break;

src/regions_bed.c

@@ -52,7 +52,7 @@ regions_bed_txt *regions_bed_init(FILE *fp, contigs_t *c)
   i = 0;
   prev_contig = prev_start = prev_end = -1;
   while(0 < fscanf(fp, "%1023s\t%u\t%u", name, &start, &end)) {
-      len = end - start + 1;
+      len = end - start;  // BED is 0-based, half-open [start, end)
       // find the contig
       while(i < c->n && 0 != strcmp(name, c->contigs[i].name)) {
           i++;
@@ -78,8 +78,8 @@ regions_bed_txt *regions_bed_init(FILE *fp, contigs_t *c)
           exit(1);
       }
 
-      if(end - start + 1 != len) {
-          fprintf(stderr, "Warning: len != end - start + 1 [%s,%u,%u,%u]\n", name, start, end, len);
+      if(end - start != len) {
+          fprintf(stderr, "Warning: len != end - start [%s,%u,%u,%u]\n", name, start, end, len);
       }
 
       if(prev_contig == i && start <= prev_end && prev_start <= start) {