filter-bam into filter-file

[Kudostoy0u]

No description provided.

[jamesli124]

The code in _filter_file.py doesn't seem to assign a value to suffix if output _file is specified. Is this expected behavior?

input_file: BH01.hg19.mdups.chr22.bam
        whitelist_file: None
        blacklist_file: None
        output_file: BH01.hg19.mdups.chr22.filtered.bam
        min_length: 50
        max_length: 350
        quality_threshold: 30
        workers: 1
        verbose: 1     
        
Traceback (most recent call last):
  File "/Users/jamesli/Repos/FinaleToolkit/src/finaletoolkit/utils/_filter_file.py", line 111, in filter_file
    flag_filtered_bam = f'{temp_dir}/flag_filtered.{suffix}'
UnboundLocalError: local variable 'suffix' referenced before assignment

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/jamesli/anaconda3/envs/finaletoolkit/bin/finaletoolkit", line 8, in <module>
    sys.exit(main_cli())
  File "/Users/jamesli/Repos/FinaleToolkit/src/finaletoolkit/cli/main_cli.py", line 1005, in main_cli
    function(**funcargs)
  File "/Users/jamesli/Repos/FinaleToolkit/src/finaletoolkit/utils/_filter_file.py", line 145, in filter_file
    pysam.set_verbosity(save)
UnboundLocalError: local variable 'save' referenced before assignment

[Kudostoy0u]

My bad, that wasn't intended - the commit I just made should fix this.

[jamesli124]

Just approving some of my own changes, nothing to see here