Castanet failing when -PostFilt True

[AnnieJForster]

Hi Rich,

Fyi, I work with Michael and Tanya.

I have run into a few bugs in 9.2 when filtering contaminated reads ("-PostFilt True").

1. I think Michael has raised this but "-PostFilt" was not available on the command line.
2. The dictionary filtering in lines 127 and 133 in app/src/parse_bam.py I think cancel each other out producing an empty read list, and then an empty bam.

 dat = {k: v for k, v in dat.items() if len(v) > ## here
              self.minimum_n_filter}

  with open(self.fnames["delreads"], "w") as f:
      [f.write(f"{v[0][1]}\n") for v in dat.values()
       if len(v) <= self.minimum_n_filter] ## and here 

The samtools command filters to keep all reads in the read list, so I believe removing the final if statement above solves this.

3. Once the above is bypassed, castanet seems to stop. I think this is because of the error handling in line 136 in the same script as the samtools command does not produce the expected healthy_msg.

  out = shell(
      f"samtools view -@ {self.p['NThreads']} -b -N {self.fnames['delreads']} {self.fnames['bam']} > {self.fnames['bamfilt']}", is_test=True)
  error_handler_cli(out, self.fnames['bamfilt'], "samtools") ## run stops here

Everything ran once I'd adjusted for the above. Let me know if you need any more info.

Many thanks,

Annie

[Mayne941]

Hi Annie, many thanks for the comprehensive error report, greatly appreciated! Sounds like this isn't blocking you if it's fixed in a fork so I've staged the fix for release with V9.3, should be coming some point in late March if schedule allows.
Cheers & best - R