bx-python error working with long chromosomes in plants

[brettChapman]

Hi

I've been getting the following error when working with plant genomes. I've also flagged the error with bx-python (bxlab/bx-python#67):

inner_distance.py \
      -i Root_1.markdup.sorted.bam \
      -r RGT_Planet.bed \
      -o Root_1 \
       \
      > stdout.txt
  head -n 2 stdout.txt > Root_1.inner_distance_mean.txt
  
  inner_distance.py --version | sed -e "s/inner_distance.py //g" > rseqc.version.txt

Command exit status:
  1

Command output:
  (empty)

Command error:
  WARNING: Skipping mount /usr/local/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
  Get exon regions from RGT_Planet.bed ...
  Traceback (most recent call last):
    File "/usr/local/bin/inner_distance.py", line 95, in <module>
      main()
    File "/usr/local/bin/inner_distance.py", line 87, in main
      obj.mRNA_inner_distance(outfile=options.output_prefix,low_bound=options.lower_bound_size,up_bound=options.upper_bound_size,step=options.step_size,refbed=options.ref_gene,sample_size=options.sampleSize, q_cut = options.map_qual)
    File "/usr/local/lib/python3.7/site-packages/qcmodule/SAM.py", line 3582, in mRNA_inner_distance
      exon_bitsets = binned_bitsets_from_list(ref_exons)
    File "/usr/local/lib/python3.7/site-packages/bx/bitset_builders.py", line 143, in binned_bitsets_from_list
      last_bitset.set_range( start, end - start )
    File "lib/bx/bitset.pyx", line 216, in bx.bitset.BinnedBitSet.set_range
    File "lib/bx/bitset.pyx", line 184, in bx.bitset.bb_check_range_count
    File "lib/bx/bitset.pyx", line 180, in bx.bitset.bb_check_index
  IndexError: 537013395 is larger than the size of this BitSet (536870912).