Performance impove

[liujilei156231]

    return wps(*args)
  File "/home/liujilei/miniconda3/envs/finaletoolkit/lib/python3.9/site-packages/finaletoolkit/frag/_wps.py", line 131, in wps
    frag_ends = frag_array(input_file,
  File "/home/liujilei/miniconda3/envs/finaletoolkit/lib/python3.9/site-packages/finaletoolkit/utils/utils.py", line 455, in frag_array
    frag_list = [
  File "/home/liujilei/miniconda3/envs/finaletoolkit/lib/python3.9/site-packages/finaletoolkit/utils/utils.py", line 455, in <listcomp>
    frag_list = [
  File "/home/liujilei/miniconda3/envs/finaletoolkit/lib/python3.9/site-packages/finaletoolkit/utils/utils.py", line 309, in frag_generator
    for read in sam_file.fetch(contig, start, stop):
  File "pysam/libcalignmentfile.pyx", line 1092, in pysam.libcalignmentfile.AlignmentFile.fetch
  File "pysam/libchtslib.pyx", line 686, in pysam.libchtslib.HTSFile.parse_region
ValueError: invalid coordinates: start (149099012) > stop (146060087)

When executing finaletoolkit WPS, an error is encountered indicating an invalid region. However, identifying the specific region causing the issue is challenging. It would be helpful to include clearer and more detailed error messages.

[jamesli124]

Hi, thanks for looking at our tools. Could you share the BED file you used? We will rewrite this code to be more specific regarding the interval causing the issue. Any particular information that you would find helpful?

[jamesli124]

The pending PR will now include the name of the chromosome/contig of the interval where stop is before start, making it easier to identify the problematic interval in your BED file.

Please also feel free to look through our wiki and documentation for additional reading on file formats and usage. Lastly, I would be happy to further correspond with you further to replicate the issue in your specific case.