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[BUG] anvi-report-inversions error message fix

Open FlorianTrigodet opened this issue 2 years ago • 0 comments

Short description of the problem

When the user provides wrong bam files, the error message is not very clear. Issue spotted by @hdore.

anvi'o version

anvio dev version

Detailed description of the issue

Here is the error message:

✖ anvi-report-inversions encountered an error after 0:00:57.123876
Traceback (most recent call last):
  File "/home/hdore/github/anvio/bin/anvi-report-inversions", line 147, in <module>
    main(args)
  File "/home/hdore/github/anvio/anvio/terminal.py", line 879, in wrapper
    program_method(*args, **kwargs)
  File "/home/hdore/github/anvio/bin/anvi-report-inversions", line 26, in main
    I.process()
  File "/home/hdore/github/anvio/anvio/inversions.py", line 1238, in process
    self.process_db(entry_name, profile_db_path, bam_file_path)
  File "/home/hdore/github/anvio/anvio/inversions.py", line 409, in process_db
    true_inversions = self.get_true_inversions_in_stretch(inversion_candidates, bam_file, contig_name, start, stop)
  File "/home/hdore/github/anvio/anvio/inversions.py", line 673, in get_true_inversions_in_stretch
    reads = [r.query_sequence for r in bam_file.fetch_only(contig_name, start=start, end=stop)]
  File "/home/hdore/github/anvio/anvio/inversions.py", line 673, in <listcomp>
    reads = [r.query_sequence for r in bam_file.fetch_only(contig_name, start=start, end=stop)]
  File "/home/hdore/github/anvio/anvio/bamops.py", line 237, in fetch_only
    for read in self.fetch(contig_name, start, end):
  File "pysam/libcalignmentfile.pyx", line 1091, in pysam.libcalignmentfile.AlignmentFile.fetch
  File "pysam/libchtslib.pyx", line 685, in pysam.libchtslib.HTSFile.parse_region
ValueError: invalid contig `psb-scaff03`

FlorianTrigodet avatar Nov 02 '22 15:11 FlorianTrigodet