Merge pull request #815 from uclahs-cds/czhu-fix-call-variant

Added fuzz test log reseults
uclahs-cds · Oct 4, 2023 · 2c2022d · 2c2022d
2 parents ab47481 + f71344c
commit 2c2022d
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Showing 20 changed files with 423 additions and 4 deletions.
diff --git a/docs/files/fuzz_test_history.tsv b/docs/files/fuzz_test_history.tsv
@@ -20,3 +20,6 @@ v1.2.0	04fec22	2023-08-24	comprehensive	303743	8	0	0:00:00.592038	109.2637484121
 v1.2.0	84afd2b	2023-09-16	snv	50275	0	0	0:00:00.143654	0.3497673129907365	0:00:57.634105	120.90536684941736
 v1.2.0	84afd2b	2023-09-16	indel	49736	0	0	0:00:00.194596	0.39638610164904325	0:00:43.395730	103.01298511471816
 v1.2.0	84afd2b	2023-09-16	comprehensive	95039	1	0	0:00:00.366488	1.1783745697633377	0:00:42.658952	186.4045027067147
+v1.2.0	aca093e	2023-09-21	snv	96909	0	0	0:00:00.139143	0.3491648515251173	0:00:56.182404	117.08552498241643
+v1.2.0	aca093e	2023-09-21	indel	96810	1	0	0:00:00.184495	0.3863134944517933	0:00:42.898299	101.18628104172282
+v1.2.0	aca093e	2023-09-21	comprehensive	184432	1	0	0:00:00.348405	1.4592854473001466	0:00:41.582605	178.84322477289754
diff --git a/moPepGen/svgraph/PVGNode.py b/moPepGen/svgraph/PVGNode.py
@@ -163,6 +163,11 @@ def get_in_nodes(self) -> List[PVGNode]:
         """ Get incoming nodes as a list """
         return list(self.in_nodes)
 
+    def has_exclusive_outbond_node(self) -> bool:
+        """ The given node has exclusive outbond node """
+        return len(self.out_nodes) == 1 and \
+            len(self.get_out_nodes()[0].in_nodes) == 1
+
     def has_multiple_segments(self) -> bool:
         """ Whether the node has multiple segments, which is when the node
         is merged from several individual nodes. """
@@ -1095,14 +1100,26 @@ def any_unaccounted_downstream_cleavage_or_stop_altering(self,
         # stop and downstream cleavage gain
         if len(self.get_out_nodes()) == 1:
             downstream = self.get_out_nodes()[0]
+            boundary_node = downstream[:1]
+            b_vars = []
+            for v in boundary_node.variants:
+                if not v.upstream_cleavage_altering and not v.variant.is_circ_rna():
+                    b_vars.append(v)
+            boundary_node.variants = b_vars
             if not (downstream.seq.seq == '*' and not downstream.get_out_nodes()):
-                boundary_nodes.append(downstream[:1])
+                boundary_nodes.append(boundary_node)
 
         # upstream cleavage gain cleavage gain
         if len(self.get_in_nodes()) == 1:
             upstream = self.get_in_nodes()[0]
+            boundary_node = upstream[-1:]
+            b_vars = []
+            for v in boundary_node.variants:
+                if not v.downstream_cleavage_altering and not v.variant.is_circ_rna():
+                    b_vars.append(v)
+            boundary_node.variants = b_vars
             if upstream.seq is not None:
-                boundary_nodes.append(upstream[-1:])
+                boundary_nodes.append(boundary_node)
 
         for node in boundary_nodes:
             if node.is_missing_any_variant(variants, self):

diff --git a/moPepGen/svgraph/PeptideVariantGraph.py b/moPepGen/svgraph/PeptideVariantGraph.py
@@ -361,7 +361,11 @@ def move_downstreams(self, nodes:Iterable[PVGNode], reading_frame_index:int
         for node in nodes:
             if node.seq.seq == '*' and not node.out_nodes:
                 continue
-            if node.get_last_rf_index() != reading_frame_index:
+            if node.get_last_rf_index() != reading_frame_index \
+                    and len(node.get_out_nodes()) == 1 \
+                    and not node.has_exclusive_outbond_node() \
+                    and not len(node.get_out_nodes()[0].get_out_nodes()) == 0 \
+                    and not node.get_out_nodes()[0].get_out_nodes()[0].seq.seq == '*':
                 continue
             is_deletion_only_end = any(x.variant.type == 'Deletion' for x in node.variants) \
                 and len(node.out_nodes) == 1 \
@@ -746,7 +750,7 @@ def fit_into_cleavage_multiple_upstream(self, cur:PVGNode) -> T:
             elif len(cur.out_nodes) == 1:
                 right = cur.split_node(s, cleavage=True, cleavage_range=r)
                 _,inbridges = self.expand_forward(cur)
-                branches = {list(right.out_nodes)[0]}
+                branches = {right}
             else:
                 branches, inbridges = self.cross_join(cur, s, cleavage_range=r)
 

diff --git a/test/files/fuzz/49/annotation.gtf b/test/files/fuzz/49/annotation.gtf
@@ -0,0 +1,13 @@
+chr1	.	gene	1	1514	.	+	.	 gene_id FAKEG00000373; transcript_id FAKET00000373; protein_id FAKEP00000373;
+chr1	.	transcript	1	1514	.	+	.	 gene_id FAKEG00000373; transcript_id FAKET00000373; protein_id FAKEP00000373; is_protein_coding true;
+chr1	.	selenocysteine	892	894	.	+	.	 gene_id FAKEG00000373; transcript_id FAKET00000373; protein_id FAKEP00000373;
+chr1	.	exon	1	111	.	+	.	 gene_id FAKEG00000373; transcript_id FAKET00000373; protein_id FAKEP00000373;
+chr1	.	CDS	57	111	.	+	1	 gene_id FAKEG00000373; transcript_id FAKET00000373; protein_id FAKEP00000373;
+chr1	.	CDS	178	473	.	+	1	 gene_id FAKEG00000373; transcript_id FAKET00000373; protein_id FAKEP00000373;
+chr1	.	exon	178	473	.	+	.	 gene_id FAKEG00000373; transcript_id FAKET00000373; protein_id FAKEP00000373;
+chr1	.	CDS	813	897	.	+	2	 gene_id FAKEG00000373; transcript_id FAKET00000373; protein_id FAKEP00000373;
+chr1	.	exon	813	897	.	+	.	 gene_id FAKEG00000373; transcript_id FAKET00000373; protein_id FAKEP00000373;
+chr1	.	CDS	1280	1471	.	+	1	 gene_id FAKEG00000373; transcript_id FAKET00000373; protein_id FAKEP00000373;
+chr1	.	exon	1280	1514	.	+	.	 gene_id FAKEG00000373; transcript_id FAKET00000373; protein_id FAKEP00000373;
+chr1	.	UTR	1	56	.	+	.	 gene_id FAKEG00000373; transcript_id FAKET00000373; protein_id FAKEP00000373;
+chr1	.	UTR	1472	1514	.	+	.	 gene_id FAKEG00000373; transcript_id FAKET00000373; protein_id FAKEP00000373;
diff --git a/test/files/fuzz/49/brute_force.txt b/test/files/fuzz/49/brute_force.txt
@@ -0,0 +1,29 @@
+DRLAMCR
+DRLAMCRVR
+DRLATCEYPGLHLEFGVK
+DRLATCEYPGLHLEFGVKLS
+DRLATCVEFGVK
+DRLATCVEFGVKLS
+HYNGVNDRDRLAMCR
+HYNGVNDRDRLATCVEFGVK
+LAMCRVR
+LAMCRVRCK
+LATCEYPGLHLEFGVK
+LATCEYPGLHLEFGVKLS
+LATCVEFGVK
+LATCVEFGVKLS
+RSRPVSYM
+RSRPVSYMCR
+RSRPVSYMCRVR
+RSRPVSYV
+RSRPVSYVNIQDCI
+SKRSRPVSYM
+SKRSRPVSYMCR
+SKRSRPVSYV
+SKRSRPVSYVNIQDCI
+SRPVSYM
+SRPVSYMCR
+SRPVSYMCRVR
+SRPVSYMCRVRCK
+SRPVSYV
+SRPVSYVNIQDCI
diff --git a/test/files/fuzz/49/fake_variants.gvf b/test/files/fuzz/49/fake_variants.gvf
@@ -0,0 +1,26 @@
+##fileformat=VCFv4.2
+##mopepgen_version=1.2.0
+##parser=parseVEP
+##reference_index=
+##genome_fasta=
+##annotation_gtf=
+##source=
+##CHROM=<Description="Gene ID">
+##INFO=<ID=TRANSCRIPT_ID,Number=1,Type=String,Description="Transcript ID">
+##INFO=<ID=GENE_SYMBOL,Number=1,Type=String,Description="Gene Symbol">
+##INFO=<ID=GENOMIC_POSITION,Number=1,Type=String,Description="Genomic Position">
+##INFO=<ID=ACCEPTER_GENE_ID,Number=1,Type=String,Description="3' Accepter Transcript's Gene ID">
+##INFO=<ID=ACCEPTER_TRANSCRIPT_ID,Number=1,Type=String,Description="3' Accepter Transcript's Transcript ID">
+##INFO=<ID=ACCEPTER_POSITION,Number=1,Type=Integer,Description="Position of the break point of the 3' accepter transcript">
+##INFO=<ID=OFFSET,Number=+,Type=Integer,Description="Offsets of fragments (exons or introns)">
+##INFO=<ID=LENGTH,Number=+,Type=Integer,Description="Lengths of fragments (exons or introns)">
+##INFO=<ID=INTRON,Number=+,Type=Integer,Description="Indices of fragments that are introns">
+##INFO=<ID=START,Number=1,Type=Integer,Description="Start Position">
+##INFO=<ID=END,Number=1,Type=Integer,Description="End Position">
+##INFO=<ID=DONOR_START,Number=1,Type=Integer,Description="Donor Start Position">
+##INFO=<ID=DONOR_END,Number=1,Type=Integer,Description="Donor End Position">
+##INFO=<ID=COORDINATE,Number=1,Type=String,Description="Coordinate for Insertion or Substitution">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+FAKEG00000373	1439	FAKEG00000373-1438-AAC-A	AAC	A	.	.	TRANSCRIPT_ID=FAKET00000373;GENOMIC_POSITION=chrF-1438:1441;GENE_SYMBOL=
+FAKEG00000373	1468	FAKEG00000373-1467-T-TAC	T	TAC	.	.	TRANSCRIPT_ID=FAKET00000373;GENOMIC_POSITION=chrF-1467:1468;GENE_SYMBOL=
+FAKEG00000373	1473	FAKEG00000373-1472-GAATATCCAGGATTGCATC-G	GAATATCCAGGATTGCATC	G	.	.	TRANSCRIPT_ID=FAKET00000373;GENOMIC_POSITION=chrF-1472:1491;GENE_SYMBOL=
diff --git a/test/files/fuzz/49/genome.fasta b/test/files/fuzz/49/genome.fasta
@@ -0,0 +1,27 @@
+>chr1
+GTGTGCCTTAAGACAGCTTTCCGTGATTGTGCGGACCACTGCCGCCACTCGCCAATTATG
+TGGGCTGAGACGGAGGGGTCGGGGAAATGTGTCGCTGCCAACCTCAATTATCGCTTTCCC
+CTGGATGCCCCAAGGCCGGTGGACTCGATTAAGGGAATGAGTCTGACTTAGCTTACATGT
+TCATACTTCCGCGATTGTACGACATGTACGAGCTTTAGTGCTATTCGTAATAAGAACTTC
+TCGGAGATTCAGCCAGTTCATCTTGTCCAACTTGTATCGTCAAATCTGAGGATGAGAGGT
+GCTCATAACCATCAGATAAGAGCGTTTCTTTTTCCTAGGTTTAGAGTACTGCCTTGGGAA
+ACGGGGCTAGCAGTAGGCGGGACTAAGAGAGCCGTCGCATCGATTACCGCTCACTGCTCT
+GAGCTTCCTAGAAATAACACCTACGCCTGTCTATCCCAGCTGTATATTATTTGGCACTAA
+CTTAGCGCCACTAGCATTAACTGGGAGACCTCATTAATTATAGGGGAGTTCGAGTCTTTG
+CACAAGTGGGAACAGCTATTTATGCTTGGCTAGCTAAGACGGCCCTAACTATGGGTGTAT
+CCCCGACCTTCGGTGGTCTGTGGATTTGAACATACGCGGCTAGAGAGCGCATACGCCCAG
+ACATCTTCAGTTATTGACCACGTTCGGTTGTTGACTCACTCTGCCGTTGGAGCCCCAAGT
+TGGATAACCACGAGATTCGCATAGCTCATTATAGGATCGTTAATGGACGCGTTATTAGAC
+TGGGCAAGTGATGGGTTTTAGGTGAGCGGATGCTGGAGATCCATTATAAATAACGTGCGA
+CGAAATCCACTCTGCACTCTTTTAGGCCAATACAGGCGGCCAACGCCGATATGAACTCCT
+TTTGTCCTGAACGCGGCCACGCTATTGGAGAACGCGGAAACCCTACATCTTGTGAGCATT
+TGGACCAGCAAATCGTTGTTGACGATCGTGATTTGACCCGGAAAATACATCTAATGGATT
+TACATTATTATTCGTTCTCTATATGACCCTAAGAGAGTCATGCATAGTCTTACCATTTCT
+CTGAATATCATGATCCATTCAGGTAAAGTAAGGCTGATTGAATTGATCGGGTGAGTTGGA
+CCCACGTCTGATGCCAGCCAAAATTGGAATCCCAGAAAAATCATCGTAAATTCAGCATCA
+AACGCGTCGTGGGGACGATGGTCATAGCCGTGGGAGCTCTCCCGTAACTTTATCACAATG
+ATGGGGCCGTCACTATACTGGTATTACATGGCTCAGGCGATTACAAGGCTGGTCGTGTGC
+GACGGACGATACCGCCGCCTCGCCCGTGCACTCGAGTTCTTTTAAGAACTCAGGAAGGAG
+GCCTATGTTTGCTCGACAAAGGACCAACAAGTCTTATAAGAGTCGTCGTCGGCATTATAA
+CGGAGTAAACGATCGCGACCGGTTAGCTATGTGAATATCCAGGATTGCATCTAGAGTTCG
+GTGTAAAATTAAGT
diff --git a/test/files/fuzz/49/proteome.fasta b/test/files/fuzz/49/proteome.fasta
@@ -0,0 +1,5 @@
+>FAKEP00000373|FAKET00000373|FAKEG00000373|XXX
+MWAETEGSGKCVAANLNYCSYFRDCTTCTSFSAIRNKNFSEIQPVHLVQLVSSNLRMRGA
+HNHQIRAFLFPRFRVLPWETGLAVGGTKRAVASITAHCSELPRNNTYACLSQLYIICWRS
+IINNVRRNPLCTLLGQYRRPTPIUTGITWLRRLQGWSCATDDTAASPVHSSSFKNSGRRP
+MFARQRTNKSYKSRRRHYNGVNDRDRLAM
diff --git a/test/files/fuzz/50/annotation.gtf b/test/files/fuzz/50/annotation.gtf
@@ -0,0 +1,5 @@
+chr1	.	gene	1	584	.	+	.	 gene_id FAKEG00000416; transcript_id FAKET00000416; protein_id FAKEP00000416;
+chr1	.	transcript	1	584	.	+	.	 gene_id FAKEG00000416; transcript_id FAKET00000416; protein_id FAKEP00000416; is_protein_coding false;
+chr1	.	exon	1	130	.	+	.	 gene_id FAKEG00000416; transcript_id FAKET00000416; protein_id FAKEP00000416;
+chr1	.	exon	180	238	.	+	.	 gene_id FAKEG00000416; transcript_id FAKET00000416; protein_id FAKEP00000416;
+chr1	.	exon	410	584	.	+	.	 gene_id FAKEG00000416; transcript_id FAKET00000416; protein_id FAKEP00000416;
diff --git a/test/files/fuzz/50/brute_force.txt b/test/files/fuzz/50/brute_force.txt
@@ -0,0 +1,29 @@
+DWASDPTGQ
+DWRHCLK
+DWRHCLKR
+GFRPHWAVMR
+GFRPHWAVMRDLYG
+HCLKRYNK
+HPSDGLATLSEALQ
+HPSDGLAYSPAPRLTDFIECVTHK
+HPSDGLAYSPAPRLTDFIECVTHKR
+HPSDGLGFRPHWAVMR
+HPSDGLGFRPHWAVMRDLYG
+LFTCSSFNGFHR
+LFTCSSFNGFHRVR
+LFTCSSFNGFHRVRDA
+LFTCSSFNGLS
+LTDFIECVTHK
+LTDFIECVTHKR
+LTDFIECVTHKRGFRPHWAVMR
+MDWASDPTGQ
+MDWRHCLK
+MDWRHCLKR
+RGFRPHWAVMR
+RGFRPHWAVMRDLYG
+RYNKVAK
+VAKLFTCSSFNGFHR
+VAKLFTCSSFNGFHRVR
+VAKLFTCSSFNGLS
+YNKVAKLFTCSSFNGFHR
+YNKVAKLFTCSSFNGLS
diff --git a/test/files/fuzz/50/fake_variants.gvf b/test/files/fuzz/50/fake_variants.gvf
@@ -0,0 +1,27 @@
+##fileformat=VCFv4.2
+##mopepgen_version=1.2.0
+##parser=parseVEP
+##reference_index=
+##genome_fasta=
+##annotation_gtf=
+##source=
+##CHROM=<Description="Gene ID">
+##INFO=<ID=TRANSCRIPT_ID,Number=1,Type=String,Description="Transcript ID">
+##INFO=<ID=GENE_SYMBOL,Number=1,Type=String,Description="Gene Symbol">
+##INFO=<ID=GENOMIC_POSITION,Number=1,Type=String,Description="Genomic Position">
+##INFO=<ID=ACCEPTER_GENE_ID,Number=1,Type=String,Description="3' Accepter Transcript's Gene ID">
+##INFO=<ID=ACCEPTER_TRANSCRIPT_ID,Number=1,Type=String,Description="3' Accepter Transcript's Transcript ID">
+##INFO=<ID=ACCEPTER_POSITION,Number=1,Type=Integer,Description="Position of the break point of the 3' accepter transcript">
+##INFO=<ID=DONOR_START,Number=1,Type=Integer,Description="Donor Start Position">
+##INFO=<ID=DONOR_END,Number=1,Type=Integer,Description="Donor End Position">
+##INFO=<ID=START,Number=1,Type=Integer,Description="Start Position">
+##INFO=<ID=END,Number=1,Type=Integer,Description="End Position">
+##INFO=<ID=COORDINATE,Number=1,Type=String,Description="Coordinate for Insertion or Substitution">
+##INFO=<ID=OFFSET,Number=+,Type=Integer,Description="Offsets of fragments (exons or introns)">
+##INFO=<ID=LENGTH,Number=+,Type=Integer,Description="Lengths of fragments (exons or introns)">
+##INFO=<ID=INTRON,Number=+,Type=Integer,Description="Indices of fragments that are introns">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+FAKEG00000416	130	RI_195-236	C	<DEL>	.	.	TRANSCRIPT_ID=FAKET00000416;START=196;END=236;GENE_SYMBOL=;GENOMIC_POSITION=chrF:196:236
+FAKEG00000416	130	A3SS_129-144-179	C	<INS>	.	.	TRANSCRIPT_ID=FAKET00000416;DONOR_START=145;DONOR_END=179;DONOR_GENE_ID=FAKEG00000416;GENE_SYMBOL=;GENOMIC_POSITION=chrF:145:179
+FAKEG00000416	206	FAKEG00000416-205-AC-A	AC	A	.	.	TRANSCRIPT_ID=FAKET00000416;GENOMIC_POSITION=chrF-205:207;GENE_SYMBOL=
+FAKEG00000416	238	A5SS_567-584	A	<DEL>	.	.	TRANSCRIPT_ID=FAKET00000416;START=568;END=584;GENE_SYMBOL=;GENOMIC_POSITION=chrF:568:584
diff --git a/test/files/fuzz/50/genome.fasta b/test/files/fuzz/50/genome.fasta
@@ -0,0 +1,11 @@
+>chr1
+CTCGTTCTCAGCGCCCGCTGGGTTTGCATTTCTGCTAGAGTTGCGGCCTTGGACTGCACA
+TGTTCGCTCCGACTCCAACGCTCGCTGTCCAGCCTGGAGAGTCTCATAAGCATCCGAGCG
+ATGGACTGGCCGCGAATCGTGAGGGACATTGTCTGAAGCGCTACAATAAAGTGGCAAAGC
+TATTCACCTGCTCCTCGTTTAACGGACTTTCATAGAGTGCGTGACGCATAAGCGAGGCTC
+GGCACTTAGGTTACCTTTCGCTTATACCAAGTCTGAGAGTGAAAGCCGCCTAAGTTGATG
+CCAGCGCTAGATGGTCAGAGCAGATGGTCACGATAGAGCGTGGCTCATGCAATCCGAGTT
+ATGCTAAGTAAACCCGTCCGGGTCAAAGCGGACTTCAGCTGATGATTGGTTCCGACCCCA
+CTGGGCAGTGATGCGAGACCTTTACGGATAAGAGGGGGGCGTCTGTTGGATGAGGCCCAT
+GCACCGCGCCTATGCCCCTATAACGCCCACGGTTGATAACGCGAGGTCGCAGCGGAAAAT
+ATCCTCTTGATTGTCACATTTGGCGCTAGATTCAGAAGATTAAT
diff --git a/test/files/fuzz/50/proteome.fasta b/test/files/fuzz/50/proteome.fasta
diff --git a/test/files/fuzz/51/annotation.gtf b/test/files/fuzz/51/annotation.gtf
@@ -0,0 +1,14 @@
+chr1	.	gene	1	1115	.	+	.	 gene_id FAKEG00000399; transcript_id FAKET00000399; protein_id FAKEP00000399;
+chr1	.	transcript	1	1115	.	+	.	 gene_id FAKEG00000399; transcript_id FAKET00000399; protein_id FAKEP00000399; is_protein_coding true;
+chr1	.	selenocysteine	806	808	.	+	.	 gene_id FAKEG00000399; transcript_id FAKET00000399; protein_id FAKEP00000399;
+chr1	.	selenocysteine	1047	1049	.	+	.	 gene_id FAKEG00000399; transcript_id FAKET00000399; protein_id FAKEP00000399;
+chr1	.	exon	1	131	.	+	.	 gene_id FAKEG00000399; transcript_id FAKET00000399; protein_id FAKEP00000399;
+chr1	.	CDS	99	131	.	+	1	 gene_id FAKEG00000399; transcript_id FAKET00000399; protein_id FAKEP00000399;
+chr1	.	CDS	248	371	.	+	2	 gene_id FAKEG00000399; transcript_id FAKET00000399; protein_id FAKEP00000399;
+chr1	.	exon	248	371	.	+	.	 gene_id FAKEG00000399; transcript_id FAKET00000399; protein_id FAKEP00000399;
+chr1	.	CDS	770	925	.	+	1	 gene_id FAKEG00000399; transcript_id FAKET00000399; protein_id FAKEP00000399;
+chr1	.	exon	770	925	.	+	.	 gene_id FAKEG00000399; transcript_id FAKET00000399; protein_id FAKEP00000399;
+chr1	.	CDS	1008	1067	.	+	1	 gene_id FAKEG00000399; transcript_id FAKET00000399; protein_id FAKEP00000399;
+chr1	.	exon	1008	1115	.	+	.	 gene_id FAKEG00000399; transcript_id FAKET00000399; protein_id FAKEP00000399;
+chr1	.	UTR	1	98	.	+	.	 gene_id FAKEG00000399; transcript_id FAKET00000399; protein_id FAKEP00000399;
+chr1	.	UTR	1068	1115	.	+	.	 gene_id FAKEG00000399; transcript_id FAKET00000399; protein_id FAKEP00000399;
diff --git a/test/files/fuzz/51/brute_force.txt b/test/files/fuzz/51/brute_force.txt
@@ -0,0 +1,99 @@
+AIELSVCSAYAGPKQK
+AIELSVCSAYAGPKQKFFPTITGR
+AIELSVCSAYAGPKQKFFPTTTGR
+AIELSVCSAYAGPKQNFFPTTTGR
+AIELSVCSAYAGPKQNFFPTTTGRK
+AIELSVYSAYAGPK
+AIELSVYSAYAGPKQK
+AIELSVYSAYAGPKQKFFPTITGR
+AIELSVYSAYAGPKQKFFPTTTGR
+AIELSVYSAYAGPKQNFFPTITGR
+AIELSVYSAYAGPKQNFFPTITGRK
+AIELSVYSAYAGPKQNFFPTTTGR
+AIELSVYSAYAGPKQNFFPTTTGRK
+ARRGDHSILNNDDDR
+AVKGGAR
+AVKGGARLTR
+FFPTITGR
+FFPTITGRK
+FFPTITGRKATSHSDTR
+FFPTTTGR
+FFPTTTGRK
+FFPTTTGRKATSHSDTR
+GDHSILNNDDDR
+GDHSILNNDDDRAVK
+GDHSILNNDDDRAVKGGAR
+GGARLTR
+GGARLTRR
+GSQLSQWHVAVTTQF
+LDRSRSFFLP
+LDRSRSFFLPQR
+LDRSRTFFLP
+LDRSRTFFLPQR
+LDSKGSQLSQWHVAVTTQF
+LLHIQILD
+LRLDSKGSQLSQWHVAVTTQF
+LTRRGPIR
+MAIELSVCSAYAGPKQK
+MAIELSVCSAYAGPKQKFFPTITGR
+MAIELSVCSAYAGPKQKFFPTTTGR
+MAIELSVCSAYAGPKQNFFPTTTGR
+MAIELSVYSAYAGPK
+MAIELSVYSAYAGPKQK
+MAIELSVYSAYAGPKQKFFPTITGR
+MAIELSVYSAYAGPKQKFFPTTTGR
+MAIELSVYSAYAGPKQNFFPTITGR
+MAIELSVYSAYAGPKQNFFPTTTGR
+MARRGDHSILNNDDDR
+MLDRSRSFFLP
+MLDRSRSFFLPQR
+MLDRSRTFFLP
+MLDRSRTFFLPQR
+MTGRWPLNCLSIVPMLDR
+MTGRWPLNCLSIVPMLDRSR
+MTGRWPLNCLSVVPMLDR
+MTGRWPLNCLSVVPMLDRSR
+QKFFPTITGR
+QKFFPTITGRK
+QKFFPTTTGR
+QKFFPTTTGRK
+QNFFPTTTGR
+QNFFPTTTGRK
+QNFFPTTTGRKATSHSDTR
+RGDHSILNNDDDR
+RGDHSILNNDDDRAVK
+RRSFANTFYR
+RSFANTFYR
+RSFANTFYRYR
+SFANTFYR
+SFANTFYRYR
+SFANTFYRYRAT
+SFFLPQR
+SFFLPQRVER
+SFFLPQRVERLLHIQILD
+SRSFFLP
+SRSFFLPQR
+SRSFFLPQRVER
+SRTFFLP
+SRTFFLPQR
+SRTFFLPQRVER
+TFFLPQR
+TFFLPQRVER
+TFFLPQRVERLLHIQILD
+TGRWPLNCLSIVPMLDR
+TGRWPLNCLSIVPMLDRSR
+TGRWPLNCLSVVPMLDR
+TGRWPLNCLSVVPMLDRSR
+VERLLHIQILD
+WPLNCLSIVPMLDR
+WPLNCLSIVPMLDRSR
+WPLNCLSIVPMLDRSRSFFLP
+WPLNCLSIVPMLDRSRSFFLPQR
+WPLNCLSIVPMLDRSRTFFLP
+WPLNCLSIVPMLDRSRTFFLPQR
+WPLNCLSVVPMLDR
+WPLNCLSVVPMLDRSR
+WPLNCLSVVPMLDRSRSFFLP
+WPLNCLSVVPMLDRSRSFFLPQR
+WPLNCLSVVPMLDRSRTFFLP
+WPLNCLSVVPMLDRSRTFFLPQR
diff --git a/test/files/fuzz/51/fake_circ_rna.gvf b/test/files/fuzz/51/fake_circ_rna.gvf
@@ -0,0 +1,25 @@
+##fileformat=VCFv4.2
+##mopepgen_version=1.2.0
+##parser=parseCIRCexplorer
+##reference_index=
+##genome_fasta=
+##annotation_gtf=
+##source=
+##CHROM=<Description="Gene ID">
+##INFO=<ID=TRANSCRIPT_ID,Number=1,Type=String,Description="Transcript ID">
+##INFO=<ID=GENE_SYMBOL,Number=1,Type=String,Description="Gene Symbol">
+##INFO=<ID=GENOMIC_POSITION,Number=1,Type=String,Description="Genomic Position">
+##INFO=<ID=OFFSET,Number=+,Type=Integer,Description="Offsets of fragments (exons or introns)">
+##INFO=<ID=LENGTH,Number=+,Type=Integer,Description="Lengths of fragments (exons or introns)">
+##INFO=<ID=INTRON,Number=+,Type=Integer,Description="Indices of fragments that are introns">
+##INFO=<ID=ACCEPTER_GENE_ID,Number=1,Type=String,Description="3' Accepter Transcript's Gene ID">
+##INFO=<ID=ACCEPTER_TRANSCRIPT_ID,Number=1,Type=String,Description="3' Accepter Transcript's Transcript ID">
+##INFO=<ID=ACCEPTER_POSITION,Number=1,Type=Integer,Description="Position of the break point of the 3' accepter transcript">
+##INFO=<ID=DONOR_START,Number=1,Type=Integer,Description="Donor Start Position">
+##INFO=<ID=DONOR_END,Number=1,Type=Integer,Description="Donor End Position">
+##INFO=<ID=START,Number=1,Type=Integer,Description="Start Position">
+##INFO=<ID=END,Number=1,Type=Integer,Description="End Position">
+##INFO=<ID=COORDINATE,Number=1,Type=String,Description="Coordinate for Insertion or Substitution">
+##POS=<Description="Gene coordinate of circRNA start">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+FAKEG00000399	0	CIRC-FAKET00000399-E1-E2-E3	.	.	.	.	OFFSET=0,247,769;LENGTH=131,124,156;INTRON=;TRANSCRIPT_ID=FAKET00000399;GENE_SYMBOL=;GENOMIC_POSITION=chrF:0