bedtools intersect false positive namecheck warning

[mdkeehan]

Thanks for bedtools it is just so handy!

Here is a small issue I have encountered with bedtools.
I am working with a genome which has successfully assembled chromosomes and also unlocalized scaffolds which we are working with. We have combined them into one big reference. The naming convention for the chromosomes is lowercase "chr" as the prefix while the unlocalized have names like "Leftover_ScbfJmS_1".
Mixing the convention in one bed file generates the namecheck warning. Here is a cut'n'paste test to generate the warning.

bedtools version

someone@somemachine:/somedir$ bedtools -version
bedtools v2.27.1-2-ge5ad7e4

False positive scary warning

someone@somemachine:/somedir$ bedtools intersect  -a tiny.chrNametest.bed -b tiny.chrNametest.bed -f 0.9 -r 
***** WARNING: File tiny.chrNametest.bed has inconsistent naming convention for record:
Leftover_ScbfJmS_1	0	25561

chrX	0	139009144
chrY	0	43300181
chrM	0	16340
Leftover_ScbfJmS_1	0	25561
Leftover_ScbfJmS_10	0	5566
Leftover_ScbfJmS_100	0	24335
Leftover_ScbfJmS_1000	0	41467
***** WARNING: File tiny.chrNametest.bed has inconsistent naming convention for record:
Leftover_ScbfJmS_1	0	25561

Remove warning with nonamecheck

someone@somemachine:/somedir$ bedtools intersect  -a tiny.chrNametest.bed -b tiny.chrNametest.bed -f 0.9 -r -nonamecheck
chrX	0	139009144
chrY	0	43300181
chrM	0	16340
Leftover_ScbfJmS_1	0	25561
Leftover_ScbfJmS_10	0	5566
Leftover_ScbfJmS_100	0	24335
Leftover_ScbfJmS_1000	0	41467

Tiny sample data to replicate the issue and use as a test case

someone@somemachine:/somedir$ cat tiny.chrNametest.bed 
chrX	0	139009144
chrY	0	43300181
chrM	0	16340
Leftover_ScbfJmS_1	0	25561
Leftover_ScbfJmS_10	0	5566
Leftover_ScbfJmS_100	0	24335
Leftover_ScbfJmS_1000	0	41467
someone@somemachine:/somedir

I think the namecheck logic needs to be improved.
The -nonamecheck makes the problem go away but ideally it wouldn't have happened in this circumstance.
It's not a big problem but the warning is worrisome and I hope the feedback makes bedtools better.
Mike