Removing unmapped contigs

[RSWilson1]

Fixes error creating IGV reports

Removed entries in BED with contigs which don't map to chromosome.
i.e. NT_ ow NW_ prefixed contigs see: https://hgvs-nomenclature.org/stable/background/refseq/.

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This change is 

[pep8speaks]

Hello @RSWilson1! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file gene_annotation2bed.py:

Line 854:80: E501 line too long (95 > 79 characters)
Line 858:80: E501 line too long (88 > 79 characters)
Line 859:80: E501 line too long (92 > 79 characters)

Comment last updated at 2024-08-02 13:22:51 UTC

[jethror1]

Reviewed 1 of 2 files at r1, 1 of 1 files at r2, all commit messages.
Reviewable status: 2 of 3 files reviewed, 1 unresolved discussion (waiting on @RSWilson1)

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gene_annotation2bed.py line 859 at r2 (raw file):

    for contig in unknown_contigs["chromosome"].unique():
        print(contig)
    print(f"Total unknown contig rows: {len(unknown_contigs)}")

since these are being removed can you make the message to the user explicit to say they have been omitted from the output

Code quote:

    print(f"Total unknown contig rows: {len(unknown_contigs)}")

[jethror1]

Reviewed 1 of 1 files at r3, all commit messages.
Reviewable status: all files reviewed, 1 unresolved discussion (waiting on @RSWilson1)

[jethror1]

Reviewable status: all files reviewed, 1 unresolved discussion (waiting on @RSWilson1)