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fix: test files added
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‎test/files/fuzz/55/annotation.gtf‎

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chrF . gene 1 462 . - . gene_id FAKEG00000361; transcript_id FAKET00000361; protein_id FAKEP00000361;
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chrF . transcript 1 462 . - . gene_id FAKEG00000361; transcript_id FAKET00000361; protein_id FAKEP00000361; is_protein_coding true;
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chrF . selenocysteine 257 259 . - . gene_id FAKEG00000361; transcript_id FAKET00000361; protein_id FAKEP00000361;
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chrF . selenocysteine 197 199 . - . gene_id FAKEG00000361; transcript_id FAKET00000361; protein_id FAKEP00000361;
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chrF . exon 1 11 . - . gene_id FAKEG00000361; transcript_id FAKET00000361; protein_id FAKEP00000361;
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chrF . CDS 3 11 . - 1 gene_id FAKEG00000361; transcript_id FAKET00000361; protein_id FAKEP00000361;
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chrF . CDS 50 264 . - 0 gene_id FAKEG00000361; transcript_id FAKET00000361; protein_id FAKEP00000361;
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chrF . exon 50 264 . - . gene_id FAKEG00000361; transcript_id FAKET00000361; protein_id FAKEP00000361;
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chrF . CDS 445 457 . - 0 gene_id FAKEG00000361; transcript_id FAKET00000361; protein_id FAKEP00000361;
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chrF . exon 445 462 . - . gene_id FAKEG00000361; transcript_id FAKET00000361; protein_id FAKEP00000361;
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chrF . UTR 1 2 . - . gene_id FAKEG00000361; transcript_id FAKET00000361; protein_id FAKEP00000361;
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chrF . UTR 458 462 . - . gene_id FAKEG00000361; transcript_id FAKET00000361; protein_id FAKEP00000361;

‎test/files/fuzz/55/brute_force.txt‎

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AYQAPSR
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EVVRAYQAPSR
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MPELIEUR
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MPELIEURTVPGLLR
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MTTMIAGLACVALLTSSPLVPR
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MTTMIAGLACVALVTSSPLVPR
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MTTMIAGLACVAVLTSSPLVPR
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MTTMIAGLACVAVVTSSPLVPR
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MTTMIAGLACVVLVTSSPLVPR
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MTTMIAGLACVVVLTSSPLVPR
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MTTMIAGLACVVVVTSSPLVPR
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PELIEUR
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PELIEURTVPGLLR
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PELIEURTVPGLLRSGEQECMLYAH
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PELIEURTVPGLLRSGEQECTLYAH
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PGLIEURTVPGLLRSGEQECTLYAH
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SGEQECMLYAHUQESGHNLAGSCPR
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SGEQECTLYAH
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SGEQECTLYAHUQESGHNLAGSCPR
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SGEQECTLYAHUQESGHYLAGSCPR
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TVPGLLRSGEQECTLYAH

‎test/files/fuzz/55/fake_variants.gvf‎

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##fileformat=VCFv4.2
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##mopepgen_version=1.4.3
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##parser=parseVEP
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##reference_index=
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##genome_fasta=
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##annotation_gtf=
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##source=
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##CHROM=<Description="Gene ID">
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##INFO=<ID=TRANSCRIPT_ID,Number=1,Type=String,Description="Transcript ID">
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##INFO=<ID=GENE_SYMBOL,Number=1,Type=String,Description="Gene Symbol">
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##INFO=<ID=GENOMIC_POSITION,Number=1,Type=String,Description="Genomic Position">
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##INFO=<ID=OFFSET,Number=+,Type=Integer,Description="Offsets of fragments (exons or introns)">
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##INFO=<ID=LENGTH,Number=+,Type=Integer,Description="Lengths of fragments (exons or introns)">
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##INFO=<ID=INTRON,Number=+,Type=Integer,Description="Indices of fragments that are introns">
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##INFO=<ID=START,Number=1,Type=Integer,Description="Start Position">
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##INFO=<ID=END,Number=1,Type=Integer,Description="End Position">
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##INFO=<ID=DONOR_START,Number=1,Type=Integer,Description="Donor Start Position">
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##INFO=<ID=DONOR_END,Number=1,Type=Integer,Description="Donor End Position">
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##INFO=<ID=COORDINATE,Number=1,Type=String,Description="Coordinate for Insertion or Substitution">
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##INFO=<ID=ACCEPTER_GENE_ID,Number=1,Type=String,Description="3' Accepter Transcript's Gene ID">
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##INFO=<ID=ACCEPTER_TRANSCRIPT_ID,Number=1,Type=String,Description="3' Accepter Transcript's Transcript ID">
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##INFO=<ID=ACCEPTER_POSITION,Number=1,Type=Integer,Description="Position of the break point of the 3' accepter transcript">
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#CHROM POS ID REF ALT QUAL FILTER INFO
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FAKEG00000361 282 FAKEG00000361-281-T-A T A . . TRANSCRIPT_ID=FAKET00000361;GENOMIC_POSITION=chrF-180:181;GENE_SYMBOL=
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FAKEG00000361 371 FAKEG00000361-370-G-A G A . . TRANSCRIPT_ID=FAKET00000361;GENOMIC_POSITION=chrF-91:92;GENE_SYMBOL=
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FAKEG00000361 13 FAKEG00000361-12-G-A G A . . TRANSCRIPT_ID=FAKET00000361;GENOMIC_POSITION=chrF-449:450;GENE_SYMBOL=
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FAKEG00000361 373 FAKEG00000361-372-T-C T C . . TRANSCRIPT_ID=FAKET00000361;GENOMIC_POSITION=chrF-89:90;GENE_SYMBOL=
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FAKEG00000361 375 FAKEG00000361-374-C-G C G . . TRANSCRIPT_ID=FAKET00000361;GENOMIC_POSITION=chrF-87:88;GENE_SYMBOL=
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FAKEG00000361 319 FAKEG00000361-318-G-C G C . . TRANSCRIPT_ID=FAKET00000361;GENOMIC_POSITION=chrF-143:144;GENE_SYMBOL=
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FAKEG00000361 378 FAKEG00000361-377-C-G C G . . TRANSCRIPT_ID=FAKET00000361;GENOMIC_POSITION=chrF-84:85;GENE_SYMBOL=
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FAKEG00000361 250 FAKEG00000361-249-T-C T C . . TRANSCRIPT_ID=FAKET00000361;GENOMIC_POSITION=chrF-212:213;GENE_SYMBOL=
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FAKEG00000361 383 FAKEG00000361-382-A-T A T . . TRANSCRIPT_ID=FAKET00000361;GENOMIC_POSITION=chrF-79:80;GENE_SYMBOL=
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FAKEG00000361 314 FAKEG00000361-313-G-C G C . . TRANSCRIPT_ID=FAKET00000361;GENOMIC_POSITION=chrF-148:149;GENE_SYMBOL=

‎test/files/fuzz/55/genome.fasta‎

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>chrF
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CACCTGTCCGTACTATAGGCAAATGGTGGGGGCTCATATGGTCAACGGTGCTGTATAAGC
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GAGGCACCAGTGGGGAACTTGTTAGCAGGACCACACAGGCCAGTCCTGCTATCATAGTAG
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TCATACGAGAAGGGGCTTGATAGCCTCGCACAACCTCTCTAGGGCAGGAACCAGCTAAAT
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AGTGACCAGATTCTTGTCAGTGGGCATATAACATGCACTCCTGCTCACCTGAGCGTAGTA
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GTCCAGGGACCGTGCGTCATTCTAAGTTCCCGCTCAAGCACACTTCATGGACGCTAGACT
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GGCGCCGGCTAGGCGAATGCATTGCAGCTATCCTGGTTTAGGATCGGGGAAGTGCTGCCC
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CTCAGGGATGAACCAAGACAGCTCTAAGCCCTGTATTCAAGTCCGGCAGGGTCTCCGACG
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CGTCTATTAGGGTATAATATAGGATGAGCCCAGGCATTACGT

‎test/files/fuzz/55/proteome.fasta‎

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>FAKEP00000361|FAKET00000361|FAKEG00000361|XXX
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MPGLIEURTVPGLLRSGEQECMLYAHUQESGHYLAGSCPREVVRGYQAPSRMTTMIAGLA
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CVVLLTSSPLVPRLYSTDR

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