Add support for converting gtf/gff3 files

[creisle]

closes: #302

[codecov[bot]]

Codecov Report

Merging #304 (0c0f051) into develop_v3 (841c364) will decrease coverage by 0.02%. The diff coverage is n/a.

@@              Coverage Diff               @@
##           develop_v3     #304      +/-   ##
==============================================
- Coverage       87.12%   87.10%   -0.03%     
==============================================
  Files              53       53              
  Lines            8831     8831              
  Branches         2291     2291              
==============================================
- Hits             7694     7692       -2     
- Misses            691      692       +1     
- Partials          446      447       +1     

Flag	Coverage Δ
unittests	87.10% <ø> (-0.03%)	:arrow_down:

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
src/mavis/breakpoint.py	90.64% <0.00%> (-0.65%)	:arrow_down:

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[zhemingfan]

From internal testing: generated KeyError: 'failed to find parent transcript (unassigned_transcript_1) skipping cds on line (2908226)' with entries: chr1_KI270713v1_random ensembl exon 35407 35916 . + . gene_id "ENSG00000268674"; gene_version "2"; transcript_id "ENST00000601199"; transcript_version "2"; exon_number "1"; gene_name "AC213203.1"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "AC213203.1-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; exon_id "ENSE00003108086"; exon_version "2"; tag "basic"; transcript_support_level "NA"; gene_type "protein_coding" ;