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static const string kCDSoverlapTRNA = "[n] Bioseq[s] [has] coding regions that overlap tRNAs" static constexpr CDiscrepancyCaseProps s_testcase_props_CDS_TRNA_OVERLAP = { CDiscrepancyVisitorImpl<eTestNames:: CDS_TRNA_OVERLAP >::Create, eTestTypes:: SEQUENCE , eTestNames:: CDS_TRNA_OVERLAP , "CDS_TRNA_OVERLAP" , "CDS tRNA Overlap" , eDisc | eSubmitter | eSmart , nullptr } static const string kCdsTrnaOverlapComment = "TAA stop codon is completed by the addition of 3' A residues to the mRNA" static constexpr CDiscrepancyCaseProps s_testcase_props__CDS_TRNA_OVERLAP = { CDiscrepancyVisitorImpl<eTestNames:: _CDS_TRNA_OVERLAP >::Create, eTestTypes:: SEQUENCE , eTestNames:: _CDS_TRNA_OVERLAP , "_CDS_TRNA_OVERLAP" , "CDS tRNA Overlap - autofix" , 0 , nullptr } const string kCDSRNAAnyOverlap = "[n/2] coding region[s] overlap RNA feature[s]" const string kCDSRNAExactMatch = "[n/2] coding region location[s] exactly match an RNA location" const string kCDSRNAContainedIn = "[n/2] coding region[s] [is] completely contained in RNA[s]" const string kCDSRNAContains = "[n/2] coding region[s] completely contain RNA[s]" const string kCDSRNAContainstRNA = "[n/2] coding region[s] completely contain tRNA[s]" const string kCDSRNAOverlapNoContain = "[n/2] coding regions overlap RNA[s] (no containment)" const string kCDSRNAOverlapNoContainSameStrand = "[n/2] coding region[s] overlap RNA[s] on the same strand (no containment)" const string kCDSRNAOverlapNoContainOppStrand = "[n/2] coding region[s] overlap RNA[s] on the opposite strand (no containment)" static constexpr CDiscrepancyCaseProps s_testcase_props_RNA_CDS_OVERLAP = { CDiscrepancyVisitorImpl<eTestNames:: RNA_CDS_OVERLAP >::Create, eTestTypes:: SEQUENCE , eTestNames:: RNA_CDS_OVERLAP , "RNA_CDS_OVERLAP" , "CDS RNA Overlap" , eDisc | eSubmitter | eSmart | eFatal , nullptr } static constexpr CDiscrepancyCaseProps s_testcase_props_OVERLAPPING_RRNAS = { CDiscrepancyVisitorImpl<eTestNames:: OVERLAPPING_RRNAS >::Create, eTestTypes:: SEQUENCE , eTestNames:: OVERLAPPING_RRNAS , "OVERLAPPING_RRNAS" , "Overlapping rRNAs" , eDisc | eSubmitter | eSmart | eFatal , nullptr } static constexpr CDiscrepancyCaseProps s_testcase_props_OVERLAPPING_GENES = { CDiscrepancyVisitorImpl<eTestNames:: OVERLAPPING_GENES >::Create, eTestTypes:: SEQUENCE , eTestNames:: OVERLAPPING_GENES , "OVERLAPPING_GENES" , "Overlapping Genes" , eDisc , nullptr } static constexpr CDiscrepancyCaseProps s_testcase_props_FIND_OVERLAPPED_GENES = { CDiscrepancyVisitorImpl<eTestNames:: FIND_OVERLAPPED_GENES >::Create, eTestTypes:: SEQUENCE , eTestNames:: FIND_OVERLAPPED_GENES , "FIND_OVERLAPPED_GENES" , "Genes completely contained by another gene on the same strand" , eDisc | eSmart , nullptr } static constexpr CDiscrepancyCaseProps s_testcase_props_DUP_GENES_OPPOSITE_STRANDS = { CDiscrepancyVisitorImpl<eTestNames:: DUP_GENES_OPPOSITE_STRANDS >::Create, eTestTypes:: SEQUENCE , eTestNames:: DUP_GENES_OPPOSITE_STRANDS , "DUP_GENES_OPPOSITE_STRANDS" , "Genes match other genes in the same location, but on the opposite strand" , eDisc | eOncaller | eSubmitter | eSmart , nullptr } static constexpr CDiscrepancyCaseProps s_testcase_props_MRNA_OVERLAPPING_PSEUDO_GENE = { CDiscrepancyVisitorImpl<eTestNames:: MRNA_OVERLAPPING_PSEUDO_GENE >::Create, eTestTypes:: SEQUENCE , eTestNames:: MRNA_OVERLAPPING_PSEUDO_GENE , "MRNA_OVERLAPPING_PSEUDO_GENE" , "mRNA overlapping pseudo gene" , eOncaller , nullptr } static const string kIntronExon = "[n] introns and exons are incorrectly positioned" static constexpr CDiscrepancyCaseProps s_testcase_props_EXON_INTRON_CONFLICT = { CDiscrepancyVisitorImpl<eTestNames:: EXON_INTRON_CONFLICT >::Create, eTestTypes:: SEQUENCE , eTestNames:: EXON_INTRON_CONFLICT , "EXON_INTRON_CONFLICT" , "Exon and intron locations should abut (unless gene is trans-spliced)" , eOncaller | eSubmitter | eSmart , nullptr } static const string kGeneMisc = "[n] gene[s] overlap[S] with IGS misc features" static constexpr CDiscrepancyCaseProps s_testcase_props_GENE_MISC_IGS_OVERLAP = { CDiscrepancyVisitorImpl<eTestNames:: GENE_MISC_IGS_OVERLAP >::Create, eTestTypes:: SEQUENCE , eTestNames:: GENE_MISC_IGS_OVERLAP , "GENE_MISC_IGS_OVERLAP" , "Gene with misc feature overlap" , eOncaller , nullptr } static constexpr CDiscrepancyCaseProps s_testcase_props_GENE_LOCUS_MISSING = { CDiscrepancyVisitorImpl<eTestNames:: GENE_LOCUS_MISSING >::Create, eTestTypes:: SEQUENCE , eTestNames:: GENE_LOCUS_MISSING , "GENE_LOCUS_MISSING" , "Gene locus missing" , eOncaller , nullptr } ◆ CollectExonsIntrons() ◆ less() ◆ USING_SCOPE() ◆ kCDSoverlapTRNA ◆ kCDSRNAAnyOverlap ◆ kCDSRNAContainedIn ◆ kCDSRNAContains ◆ kCDSRNAContainstRNA ◆ kCDSRNAExactMatch ◆ kCDSRNAOverlapNoContain ◆ kCDSRNAOverlapNoContainOppStrand ◆ kCDSRNAOverlapNoContainSameStrand ◆ kCdsTrnaOverlapComment const string kCdsTrnaOverlapComment = "TAA stop codon is completed by the addition of 3' A residues to the mRNA" static ◆ kGeneMisc ◆ kIntronExon const string kIntronExon = "[n] introns and exons are incorrectly positioned" static ◆ s_testcase_props__CDS_TRNA_OVERLAP ◆ s_testcase_props_CDS_TRNA_OVERLAP ◆ s_testcase_props_DUP_GENES_OPPOSITE_STRANDS ◆ s_testcase_props_EXON_INTRON_CONFLICT ◆ s_testcase_props_FIND_OVERLAPPED_GENES ◆ s_testcase_props_GENE_LOCUS_MISSING ◆ s_testcase_props_GENE_MISC_IGS_OVERLAP ◆ s_testcase_props_MRNA_OVERLAPPING_PSEUDO_GENE ◆ s_testcase_props_OVERLAPPING_GENES ◆ s_testcase_props_OVERLAPPING_RRNAS ◆ s_testcase_props_RNA_CDS_OVERLAPRetroSearch is an open source project built by @garambo | Open a GitHub Issue
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