Missing bam/cram file should return an error code

[patbohn]

Hi, when running perbase base-depth with an incorrect BAM/CRAM path, even though stderr reports thread '<unnamed>' panicked at 'Indexed BAM/CRAM: FileNotFound [...] perbase/src/lib/par_granges.rs:159:72, it seems that no error code was returned (i.e. it apparently returned 0). This can be an issue when using pipeline or workload managers.

[sstadick]

Thanks for making this issue! I look into it and get an update out in the near future. That is definitely not the desired behavior, it should exit > 0.👍

[nano-pat]

Small bump - I think what's happening here is that while you're catching any Error returned here:

perbase/src/main.rs

Line 38 in abdfb75

if let Err(err) = Args::from_args().subcommand.run() {

A missing file will not return an Error, but just panic due to the .expect() call here:

perbase/src/lib/par_granges.rs

Line 159 in abdfb75

let mut reader = IndexedReader::from_path(&self.reads).expect("Indexed BAM/CRAM");

For the specific call in granges I suppose returning the Error early should work as the output of the process_region function is already a Result type.