required arguments not recognized when supplying --intervals-bed

[avril-m-harder]

Program works great when I run without a BED file:

${BESTPATH}/best sorted_pds5c_Tube01_L01.bam GCF_000001735.3_TAIR10_genomic_softmasked.fna.gz pds5c_Tube01_L01_best

But when I add a BED file for partitioning results by regions:

${BESTPATH}/best --intervals-bed GCF_000001735.3_TAIR10_genomic_softmasked.bed sorted_pds5c_Tube01_L01.bam GCF_000001735.3_TAIR10_genomic_softmasked.fna.gz pds5c_Tube01_L01_best

I get the error:

error: The following required arguments were not provided:
    <INPUT>
    <REFERENCE>
    <STATS_PREFIX>

USAGE:
    best --intervals-bed <INTERVALS_BED>... <INPUT> <REFERENCE> <STATS_PREFIX>

Thanks!

[Daniel-Liu-c0deb0t]

The --intervals-bed command can take multiple paths, so it will greedily use all the paths specified afterwards. To work around this, add --:

best --intervals-bed file.bed -- file.bam file.fna.gz output

Alternatively, you can move --intervals-bed to be the last parameter, so there's no other file paths after it.

[avril-m-harder]

Thanks! Both of those approaches give me the error:

thread 'main' panicked at 'called `Result::unwrap()` on an `Err` value: ParseIntError { kind: InvalidDigit }', src/bed.rs:47:65 note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace

[Daniel-Liu-c0deb0t]

Seems like there is an error in parsing the bed file. best expects tab separated rows in the bed file. The second and third columns should be integer coordinates. Can you double check if all of its lines are formatted correctly?

I should also update the error message to be more informative.