Pysam dispatch call to samtools index does not accept '-M' parameter from documentation

[NatPRoach]

package	version
pysam	0.20.0

When running the usage function for pysam index in the python interpreter the parameter -M is listed as a way to get it to accept multiple files to index.

Python 3.10.8 | packaged by conda-forge | (main, Nov 22 2022, 08:27:35) [Clang 14.0.6 ] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import pysam
>>> print(pysam.index.usage())
Usage: samtools index -M [-bc] [-m INT] <in1.bam> <in2.bam>...
   or: samtools index [-bc] [-m INT] <in.bam> [out.index]
Options:
  -b       Generate BAI-format index for BAM files [default]
  -c       Generate CSI-format index for BAM files
  -m INT   Set minimum interval size for CSI indices to 2^INT [14]
  -M       Interpret all filename arguments as files to be indexed
  -o FILE  Write index to FILE [alternative to <out.index> as an argument]
  -@ INT   Sets the number of threads [none]

However attempting to run pysam with this parameter results in an error.

import pysam
from pathlib import Path
from fgpyo.sam.builder import SamBuilder

builder = SamBuilder()
builder.add_pair()
builder.add_pair()

example1 = Path("example1.bam")
builder.to_path(example1)
example2 = Path("example2.bam")
builder.to_path(example2)

pysam.index("-M", str(example1), str(example2))

Results in the following error:

Traceback (most recent call last):
  File "/Users/nproach/Documents/fulcrum_genomics/internal_repos/fgpyo/mre.py", line 14, in <module>
    pysam.index("-M", str(example1), str(example2))
  File "/Users/nproach/miniconda3/envs/fgpyo-test/lib/python3.10/site-packages/pysam/utils.py", line 56, in __call__
    retval, stderr, stdout = _pysam_dispatch(
  File "pysam/libcutils.pyx", line 323, in pysam.libcutils._pysam_dispatch
OSError: No such file or directory: '-M'

[jmarshall]

Thanks for the report. Somewhat unfortunately, the Python code contains an additional option parser for the index subcommands, and that had not been updated to account for newer options added to samtools or bcftools. I've fixed this by simplifying the additional parser so that it doesn't need its own list of the simple options like -M.

This should now be fixed if you build your own pysam from the Git repository, and the fix will appear in the next pysam release.