Allow writing chrom names with . in the name

[donaldcampbelljr]

Ok, I was able to reproduce (was still using a smaller subset of chroms).

Added a print function immediately before opening each input file for the merge.

/home/drc/Downloads/gtars_74_issue/output/testchrY_NC_051844.1_shift.bed
thread 'main' panicked at src/uniwig/writing.rs:84:49:
called Result::unwrap() on an Err value: Os { code: 2, kind: NotFound, message: "No such file or directory" }

Checking the folder, I see a file: testchrY_NC_051844.bed. Checking chrom.sizes:

chrX	124992030
chrY_NC_051844.1	3937623
chrY_unplaced_NW_024010443.1	1569522

So, it appears to me that it is dropping the .1 when writing that particular chromosome to file.

Similar issue for the following chromosome: chrY_unplaced_NW_024010443.bed exists without the .1.

Originally posted by @donaldcampbelljr in #74

[nsheff]

You just need to make sure it follows the SAM spec for what's allowed in a chrom name. periods are allowed.

[donaldcampbelljr]

This was the simple fix I suspected it to be. While I was investigating, I also confirmed the code works for many other chromosome names with various symbols per the SAM spec.

Examples:
chr22.1 17820380
chr22#1 17820380
chr22$1 17820380
chr22%1 17820380
chr22&1 17820380
chr22+1 17820380
chr22_1 17820380
chr22^1 17820380
chr22~1 17820380
chr22-1 17820380

[donaldcampbelljr]

One issue:
SAM allows / but this currently causes issues when attempting to create temp files before merging.

[nleroy917]

I think slashes are very strictly forbidden in file names/systems

[nsheff]

yes, you will probably need to accommodate that, then.