Treat regions [-1,n) as [0,n) when indexing

In VCF files, 1-based POS=0 represents an event in a telomere.
POS=0 is represented as 0-based [-1,0), which previously led to a crash
during indexing.  Instead treat [-1,0) as [0,1) and larger [-1,n) as [0,n)
so that such regions will be placed in an appropriately-sized leftmost
bin.  (Treat [-1,0) slightly more specially as [0,0) winds up in bin 0.)

The previous crash occurred within insert_to_l(); this fixes the crash and
alters beg/end for [-1,n) regions for both insert_to_l() and insert_to_b().
Fixes #406.

Author: jmarshall

hts.c

@@ -1366,8 +1366,12 @@ int hts_idx_push(hts_idx_t *idx, int tid, int beg, int end, uint64_t offset, int
     if ( tid>=0 )
     {
         if (idx->bidx[tid] == 0) idx->bidx[tid] = kh_init(bin);
-        if ( is_mapped)
+        if (is_mapped) {
+            // shoehorn [-1,0) (VCF POS=0) into the leftmost bottom-level bin
+            if (beg < 0)  beg = 0;
+            if (end <= 0) end = 1;
             insert_to_l(&idx->lidx[tid], beg, end, idx->z.last_off, idx->min_shift); // last_off points to the start of the current record
+        }
     }
     else idx->n_no_coor++;
     bin = hts_reg2bin(beg, end, idx->min_shift, idx->n_lvls);