NCBI C++ ToolKit
Classes | Functions | Variables
discrepancy_case.cpp File Reference
#include <ncbi_pch.hpp>
#include "discrepancy_core.hpp"
#include "utils.hpp"
#include <objects/general/Dbtag.hpp>
#include <objects/macro/Molecule_type.hpp>
#include <objects/macro/Molecule_class_type.hpp>
#include <objects/seqfeat/Imp_feat.hpp>
#include <objects/seqfeat/RNA_gen.hpp>
#include <objects/seqfeat/SeqFeatXref.hpp>
#include <objects/seq/seqport_util.hpp>
#include <objects/macro/String_constraint.hpp>
#include <objects/misc/sequence_macros.hpp>
#include <objects/seq/MolInfo.hpp>
#include <objmgr/bioseq_ci.hpp>
#include <objmgr/feat_ci.hpp>
#include <objmgr/seq_vector.hpp>
#include <objmgr/util/feature.hpp>
#include <objmgr/bioseq_handle.hpp>
#include <objmgr/object_manager.hpp>
#include <objmgr/seqdesc_ci.hpp>
#include <sstream>
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Classes

class  CDiscrepancyPrivateData< eTestNames::GENE_PRODUCT_CONFLICT >
 

Functions

 USING_SCOPE (objects)
 
static const CSeq_idGetProteinId (const CBioseq &seq)
 
static bool StrandsMatch (ENa_strand strand1, ENa_strand strand2)
 
static bool ProductNamesAreSimilar (const string &product1, const string &product2)
 
static bool ShouldIgnore (const string &product)
 
static bool HasOverlapNote (const CSeq_feat &feat)
 
static bool SetOverlapNote (CSeq_feat &feat)
 
static string GetProdName (const CSeq_feat *feat, map< const CSeq_feat *, string > &products, CDiscrepancyContext &context)
 
static bool HasContainedNote (const CSeq_feat &feat)
 

Variables

static constexpr CDiscrepancyCaseProps s_testcase_props_COUNT_NUCLEOTIDES = { CDiscrepancyVisitorImpl<eTestNames:: COUNT_NUCLEOTIDES >::Create, eTestTypes:: SEQUENCE , eTestNames:: COUNT_NUCLEOTIDES , "COUNT_NUCLEOTIDES" , "Count nucleotide sequences" , eOncaller | eSubmitter | eSmart | eBig , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_COUNT_PROTEINS = { CDiscrepancyVisitorImpl<eTestNames:: COUNT_PROTEINS >::Create, eTestTypes:: SEQUENCE , eTestNames:: COUNT_PROTEINS , "COUNT_PROTEINS" , "Count Proteins" , eDisc , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_MISSING_PROTEIN_ID = { CDiscrepancyVisitorImpl<eTestNames:: MISSING_PROTEIN_ID >::Create, eTestTypes:: SEQUENCE , eTestNames:: MISSING_PROTEIN_ID , "MISSING_PROTEIN_ID" , "Missing Protein ID" , eDisc | eSubmitter | eSmart | eFatal , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_INCONSISTENT_PROTEIN_ID = { CDiscrepancyVisitorImpl<eTestNames:: INCONSISTENT_PROTEIN_ID >::Create, eTestTypes:: SEQUENCE , eTestNames:: INCONSISTENT_PROTEIN_ID , "INCONSISTENT_PROTEIN_ID" , "Inconsistent Protein ID" , eDisc | eSubmitter | eSmart | eFatal , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_N_RUNS = { CDiscrepancyVisitorImpl<eTestNames:: N_RUNS >::Create, eTestTypes:: SEQUENCE , eTestNames:: N_RUNS , "N_RUNS" , "More than 10 Ns in a row" , eDisc | eSubmitter | eSmart | eBig | eFatal , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_PERCENT_N = { CDiscrepancyVisitorImpl<eTestNames:: PERCENT_N >::Create, eTestTypes:: SEQUENCE , eTestNames:: PERCENT_N , "PERCENT_N" , "More than 5 percent Ns" , eDisc | eSubmitter | eSmart | eBig , nullptr }
 
static const char * kRRNASpacer [] = { "internal", "transcribed", "spacer" }
 
static const size_t kRRNASpacer_len = ArraySize(kRRNASpacer)
 
static constexpr CDiscrepancyCaseProps s_testcase_props_INTERNAL_TRANSCRIBED_SPACER_RRNA = { CDiscrepancyVisitorImpl<eTestNames:: INTERNAL_TRANSCRIBED_SPACER_RRNA >::Create, eTestTypes:: FEAT , eTestNames:: INTERNAL_TRANSCRIBED_SPACER_RRNA , "INTERNAL_TRANSCRIBED_SPACER_RRNA" , "Look for rRNAs that contain either 'internal', 'transcribed' or 'spacer'" , eOncaller , nullptr }
 
static const char * kSimilarProductWords [] = { "transposase", "integrase" }
 
static const size_t kNumSimilarProductWords = ArraySize(kSimilarProductWords)
 
static const char * kIgnoreSimilarProductWords [] = { "hypothetical protein", "phage", "predicted protein" }
 
static const size_t kNumIgnoreSimilarProductWords = ArraySize(kIgnoreSimilarProductWords)
 
static const string kOverlappingCDSNoteText = "overlaps another CDS with the same product name"
 
static const char * kOverlap0 = "[n] coding region[s] overlap[S] another coding region with a similar or identical name."
 
static const char * kOverlap1 = "[n] coding region[s] overlap[S] another coding region with a similar or identical name, but [has] the appropriate note text."
 
static const char * kOverlap2 = "[n] coding region[s] overlap[S] another coding region with a similar or identical name and [does] not have the appropriate note text."
 
static constexpr CDiscrepancyCaseProps s_testcase_props_OVERLAPPING_CDS = { CDiscrepancyVisitorImpl<eTestNames:: OVERLAPPING_CDS >::Create, eTestTypes:: SEQUENCE , eTestNames:: OVERLAPPING_CDS , "OVERLAPPING_CDS" , "Overlapping CDs" , eDisc , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_PARTIAL_CDS_COMPLETE_SEQUENCE = { CDiscrepancyVisitorImpl<eTestNames:: PARTIAL_CDS_COMPLETE_SEQUENCE >::Create, eTestTypes:: FEAT , eTestNames:: PARTIAL_CDS_COMPLETE_SEQUENCE , "PARTIAL_CDS_COMPLETE_SEQUENCE" , "Partial CDSs in Complete Sequences" , eDisc | eOncaller | eSubmitter | eSmart , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_RNA_NO_PRODUCT = { CDiscrepancyVisitorImpl<eTestNames:: RNA_NO_PRODUCT >::Create, eTestTypes:: FEAT , eTestNames:: RNA_NO_PRODUCT , "RNA_NO_PRODUCT" , "Find RNAs without Products" , eDisc | eOncaller | eSubmitter | eSmart , nullptr }
 
static const char * kContained = "[n] coding region[s] [is] completely contained in another coding region."
 
static const char * kContainedNote = "[n] coding region[s] [is] completely contained in another coding region, but have note."
 
static const char * kContainedSame = "[n] coding region[s] [is] completely contained in another coding region on the same strand."
 
static const char * kContainedOpps = "[n] coding region[s] [is] completely contained in another coding region, but on the opposite strand."
 
static constexpr CDiscrepancyCaseProps s_testcase_props_CONTAINED_CDS = { CDiscrepancyVisitorImpl<eTestNames:: CONTAINED_CDS >::Create, eTestTypes:: SEQUENCE , eTestNames:: CONTAINED_CDS , "CONTAINED_CDS" , "Contained CDs" , eDisc | eSubmitter | eSmart | eFatal , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_ZERO_BASECOUNT = { CDiscrepancyVisitorImpl<eTestNames:: ZERO_BASECOUNT >::Create, eTestTypes:: SEQUENCE , eTestNames:: ZERO_BASECOUNT , "ZERO_BASECOUNT" , "Zero Base Counts" , eDisc | eOncaller | eSubmitter | eSmart | eBig , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_NONWGS_SETS_PRESENT = { CDiscrepancyVisitorImpl<eTestNames:: NONWGS_SETS_PRESENT >::Create, eTestTypes:: SEQ_SET , eTestNames:: NONWGS_SETS_PRESENT , "NONWGS_SETS_PRESENT" , "Eco, mut, phy or pop sets present" , eDisc , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_NO_ANNOTATION = { CDiscrepancyVisitorImpl<eTestNames:: NO_ANNOTATION >::Create, eTestTypes:: SEQUENCE , eTestNames:: NO_ANNOTATION , "NO_ANNOTATION" , "No annotation" , eDisc | eOncaller | eSubmitter | eSmart | eBig , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_LONG_NO_ANNOTATION = { CDiscrepancyVisitorImpl<eTestNames:: LONG_NO_ANNOTATION >::Create, eTestTypes:: SEQUENCE , eTestNames:: LONG_NO_ANNOTATION , "LONG_NO_ANNOTATION" , "No annotation for LONG sequence" , eDisc | eOncaller | eSubmitter | eSmart | eBig , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_VERY_LONG_NO_ANNOTATION = { CDiscrepancyVisitorImpl<eTestNames:: VERY_LONG_NO_ANNOTATION >::Create, eTestTypes:: SEQUENCE , eTestNames:: VERY_LONG_NO_ANNOTATION , "VERY_LONG_NO_ANNOTATION" , "No annotation for LONG sequence" , eDisc | eOncaller | eSubmitter | eSmart | eBig , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_POSSIBLE_LINKER = { CDiscrepancyVisitorImpl<eTestNames:: POSSIBLE_LINKER >::Create, eTestTypes:: SEQUENCE , eTestNames:: POSSIBLE_LINKER , "POSSIBLE_LINKER" , "Detect linker sequence after poly-A tail" , eOncaller , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_ORDERED_LOCATION = { CDiscrepancyVisitorImpl<eTestNames:: ORDERED_LOCATION >::Create, eTestTypes:: FEAT , eTestNames:: ORDERED_LOCATION , "ORDERED_LOCATION" , "Location is ordered (intervals interspersed with gaps)" , eDisc | eOncaller | eSmart , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_MISSING_LOCUS_TAGS = { CDiscrepancyVisitorImpl<eTestNames:: MISSING_LOCUS_TAGS >::Create, eTestTypes:: SEQUENCE , eTestNames:: MISSING_LOCUS_TAGS , "MISSING_LOCUS_TAGS" , "Missing locus tags" , eDisc | eSubmitter | eSmart | eFatal , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_NO_LOCUS_TAGS = { CDiscrepancyVisitorImpl<eTestNames:: NO_LOCUS_TAGS >::Create, eTestTypes:: FEAT , eTestNames:: NO_LOCUS_TAGS , "NO_LOCUS_TAGS" , "No locus tags at all" , eDisc | eSubmitter | eSmart | eFatal , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_INCONSISTENT_LOCUS_TAG_PREFIX = { CDiscrepancyVisitorImpl<eTestNames:: INCONSISTENT_LOCUS_TAG_PREFIX >::Create, eTestTypes:: FEAT , eTestNames:: INCONSISTENT_LOCUS_TAG_PREFIX , "INCONSISTENT_LOCUS_TAG_PREFIX" , "Inconsistent locus tag prefix" , eDisc | eSubmitter | eSmart , nullptr }
 
static const string kInconsistent_Moltype = "[n] sequences have inconsistent moltypes"
 
static constexpr CDiscrepancyCaseProps s_testcase_props_INCONSISTENT_MOLTYPES = { CDiscrepancyVisitorImpl<eTestNames:: INCONSISTENT_MOLTYPES >::Create, eTestTypes:: SEQUENCE , eTestNames:: INCONSISTENT_MOLTYPES , "INCONSISTENT_MOLTYPES" , "Inconsistent molecule types" , eDisc | eOncaller | eSmart , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_BAD_LOCUS_TAG_FORMAT = { CDiscrepancyVisitorImpl<eTestNames:: BAD_LOCUS_TAG_FORMAT >::Create, eTestTypes:: SEQUENCE , eTestNames:: BAD_LOCUS_TAG_FORMAT , "BAD_LOCUS_TAG_FORMAT" , "Bad locus tag format" , eDisc | eSubmitter | eSmart , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_SEGSETS_PRESENT = { CDiscrepancyVisitorImpl<eTestNames:: SEGSETS_PRESENT >::Create, eTestTypes:: SEQ_SET , eTestNames:: SEGSETS_PRESENT , "SEGSETS_PRESENT" , "Segsets present" , eDisc | eSmart | eFatal , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_QUALITY_SCORES = { CDiscrepancyVisitorImpl<eTestNames:: QUALITY_SCORES >::Create, eTestTypes:: SEQUENCE , eTestNames:: QUALITY_SCORES , "QUALITY_SCORES" , "Check for quality scores" , eDisc | eSmart , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_BACTERIA_SHOULD_NOT_HAVE_MRNA = { CDiscrepancyVisitorImpl<eTestNames:: BACTERIA_SHOULD_NOT_HAVE_MRNA >::Create, eTestTypes:: FEAT , eTestNames:: BACTERIA_SHOULD_NOT_HAVE_MRNA , "BACTERIA_SHOULD_NOT_HAVE_MRNA" , "Bacterial sequences should not have mRNA features" , eDisc | eOncaller | eSubmitter | eSmart , nullptr }
 
static const string kDiscMessage = "[n] feature[s] contain[S] invalid BGPIPE qualifiers"
 
static constexpr CDiscrepancyCaseProps s_testcase_props_BAD_BGPIPE_QUALS = { CDiscrepancyVisitorImpl<eTestNames:: BAD_BGPIPE_QUALS >::Create, eTestTypes:: SEQUENCE , eTestNames:: BAD_BGPIPE_QUALS , "BAD_BGPIPE_QUALS" , "Bad BGPIPE qualifiers" , eDisc | eSmart , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_GENE_PRODUCT_CONFLICT = { CDiscrepancyVisitorImpl<eTestNames:: GENE_PRODUCT_CONFLICT >::Create, eTestTypes:: SEQUENCE , eTestNames:: GENE_PRODUCT_CONFLICT , "GENE_PRODUCT_CONFLICT" , "Gene Product Conflict" , eDisc | eSubmitter | eSmart , nullptr }
 

Function Documentation

◆ GetProdName()

static string GetProdName ( const CSeq_feat feat,
map< const CSeq_feat *, string > &  products,
CDiscrepancyContext context 
)
static

◆ GetProteinId()

static const CSeq_id* GetProteinId ( const CBioseq seq)
static

◆ HasContainedNote()

static bool HasContainedNote ( const CSeq_feat feat)
static

◆ HasOverlapNote()

static bool HasOverlapNote ( const CSeq_feat feat)
static

◆ ProductNamesAreSimilar()

static bool ProductNamesAreSimilar ( const string product1,
const string product2 
)
static

◆ SetOverlapNote()

static bool SetOverlapNote ( CSeq_feat feat)
static

◆ ShouldIgnore()

static bool ShouldIgnore ( const string product)
static

◆ StrandsMatch()

static bool StrandsMatch ( ENa_strand  strand1,
ENa_strand  strand2 
)
static

Definition at line 219 of file discrepancy_case.cpp.

References eNa_strand_minus.

◆ USING_SCOPE()

USING_SCOPE ( objects  )

Variable Documentation

◆ kContained

const char* kContained = "[n] coding region[s] [is] completely contained in another coding region."
static

Definition at line 471 of file discrepancy_case.cpp.

Referenced by CDiscrepancyVisitorImpl< _Name >::Summarize().

◆ kContainedNote

const char* kContainedNote = "[n] coding region[s] [is] completely contained in another coding region, but have note."
static

Definition at line 472 of file discrepancy_case.cpp.

◆ kContainedOpps

const char* kContainedOpps = "[n] coding region[s] [is] completely contained in another coding region, but on the opposite strand."
static

Definition at line 474 of file discrepancy_case.cpp.

◆ kContainedSame

const char* kContainedSame = "[n] coding region[s] [is] completely contained in another coding region on the same strand."
static

Definition at line 473 of file discrepancy_case.cpp.

◆ kDiscMessage

const string kDiscMessage = "[n] feature[s] contain[S] invalid BGPIPE qualifiers"
static

Definition at line 964 of file discrepancy_case.cpp.

◆ kIgnoreSimilarProductWords

const char* kIgnoreSimilarProductWords[] = { "hypothetical protein", "phage", "predicted protein" }
static

Definition at line 228 of file discrepancy_case.cpp.

Referenced by ProductNamesAreSimilar().

◆ kInconsistent_Moltype

const string kInconsistent_Moltype = "[n] sequences have inconsistent moltypes"
static

Definition at line 835 of file discrepancy_case.cpp.

Referenced by CDiscrepancyVisitorImpl< _Name >::Summarize().

◆ kNumIgnoreSimilarProductWords

const size_t kNumIgnoreSimilarProductWords = ArraySize(kIgnoreSimilarProductWords)
static

Definition at line 229 of file discrepancy_case.cpp.

Referenced by ProductNamesAreSimilar().

◆ kNumSimilarProductWords

const size_t kNumSimilarProductWords = ArraySize(kSimilarProductWords)
static

Definition at line 226 of file discrepancy_case.cpp.

Referenced by ProductNamesAreSimilar().

◆ kOverlap0

const char* kOverlap0 = "[n] coding region[s] overlap[S] another coding region with a similar or identical name."
static

Definition at line 297 of file discrepancy_case.cpp.

Referenced by CDiscrepancyVisitorImpl< _Name >::Summarize().

◆ kOverlap1

const char* kOverlap1 = "[n] coding region[s] overlap[S] another coding region with a similar or identical name, but [has] the appropriate note text."
static

Definition at line 298 of file discrepancy_case.cpp.

◆ kOverlap2

const char* kOverlap2 = "[n] coding region[s] overlap[S] another coding region with a similar or identical name and [does] not have the appropriate note text."
static

Definition at line 299 of file discrepancy_case.cpp.

◆ kOverlappingCDSNoteText

const string kOverlappingCDSNoteText = "overlaps another CDS with the same product name"
static

Definition at line 278 of file discrepancy_case.cpp.

Referenced by HasOverlapNote(), and SetOverlapNote().

◆ kRRNASpacer

const char* kRRNASpacer[] = { "internal", "transcribed", "spacer" }
static

Definition at line 199 of file discrepancy_case.cpp.

◆ kRRNASpacer_len

const size_t kRRNASpacer_len = ArraySize(kRRNASpacer)
static

Definition at line 200 of file discrepancy_case.cpp.

◆ kSimilarProductWords

const char* kSimilarProductWords[] = { "transposase", "integrase" }
static

Definition at line 225 of file discrepancy_case.cpp.

Referenced by ProductNamesAreSimilar().

◆ s_testcase_props_BACTERIA_SHOULD_NOT_HAVE_MRNA

constexpr CDiscrepancyCaseProps s_testcase_props_BACTERIA_SHOULD_NOT_HAVE_MRNA = { CDiscrepancyVisitorImpl<eTestNames:: BACTERIA_SHOULD_NOT_HAVE_MRNA >::Create, eTestTypes:: FEAT , eTestNames:: BACTERIA_SHOULD_NOT_HAVE_MRNA , "BACTERIA_SHOULD_NOT_HAVE_MRNA" , "Bacterial sequences should not have mRNA features" , eDisc | eOncaller | eSubmitter | eSmart , nullptr }
staticconstexpr

Definition at line 949 of file discrepancy_case.cpp.

◆ s_testcase_props_BAD_BGPIPE_QUALS

constexpr CDiscrepancyCaseProps s_testcase_props_BAD_BGPIPE_QUALS = { CDiscrepancyVisitorImpl<eTestNames:: BAD_BGPIPE_QUALS >::Create, eTestTypes:: SEQUENCE , eTestNames:: BAD_BGPIPE_QUALS , "BAD_BGPIPE_QUALS" , "Bad BGPIPE qualifiers" , eDisc | eSmart , nullptr }
staticconstexpr

Definition at line 966 of file discrepancy_case.cpp.

◆ s_testcase_props_BAD_LOCUS_TAG_FORMAT

constexpr CDiscrepancyCaseProps s_testcase_props_BAD_LOCUS_TAG_FORMAT = { CDiscrepancyVisitorImpl<eTestNames:: BAD_LOCUS_TAG_FORMAT >::Create, eTestTypes:: SEQUENCE , eTestNames:: BAD_LOCUS_TAG_FORMAT , "BAD_LOCUS_TAG_FORMAT" , "Bad locus tag format" , eDisc | eSubmitter | eSmart , nullptr }
staticconstexpr

Definition at line 869 of file discrepancy_case.cpp.

◆ s_testcase_props_CONTAINED_CDS

constexpr CDiscrepancyCaseProps s_testcase_props_CONTAINED_CDS = { CDiscrepancyVisitorImpl<eTestNames:: CONTAINED_CDS >::Create, eTestTypes:: SEQUENCE , eTestNames:: CONTAINED_CDS , "CONTAINED_CDS" , "Contained CDs" , eDisc | eSubmitter | eSmart | eFatal , nullptr }
staticconstexpr

Definition at line 477 of file discrepancy_case.cpp.

◆ s_testcase_props_COUNT_NUCLEOTIDES

constexpr CDiscrepancyCaseProps s_testcase_props_COUNT_NUCLEOTIDES = { CDiscrepancyVisitorImpl<eTestNames:: COUNT_NUCLEOTIDES >::Create, eTestTypes:: SEQUENCE , eTestNames:: COUNT_NUCLEOTIDES , "COUNT_NUCLEOTIDES" , "Count nucleotide sequences" , eOncaller | eSubmitter | eSmart | eBig , nullptr }
staticconstexpr

Definition at line 59 of file discrepancy_case.cpp.

◆ s_testcase_props_COUNT_PROTEINS

constexpr CDiscrepancyCaseProps s_testcase_props_COUNT_PROTEINS = { CDiscrepancyVisitorImpl<eTestNames:: COUNT_PROTEINS >::Create, eTestTypes:: SEQUENCE , eTestNames:: COUNT_PROTEINS , "COUNT_PROTEINS" , "Count Proteins" , eDisc , nullptr }
staticconstexpr

Definition at line 80 of file discrepancy_case.cpp.

◆ s_testcase_props_GENE_PRODUCT_CONFLICT

constexpr CDiscrepancyCaseProps s_testcase_props_GENE_PRODUCT_CONFLICT = { CDiscrepancyVisitorImpl<eTestNames:: GENE_PRODUCT_CONFLICT >::Create, eTestTypes:: SEQUENCE , eTestNames:: GENE_PRODUCT_CONFLICT , "GENE_PRODUCT_CONFLICT" , "Gene Product Conflict" , eDisc | eSubmitter | eSmart , nullptr }
staticconstexpr

Definition at line 1021 of file discrepancy_case.cpp.

◆ s_testcase_props_INCONSISTENT_LOCUS_TAG_PREFIX

constexpr CDiscrepancyCaseProps s_testcase_props_INCONSISTENT_LOCUS_TAG_PREFIX = { CDiscrepancyVisitorImpl<eTestNames:: INCONSISTENT_LOCUS_TAG_PREFIX >::Create, eTestTypes:: FEAT , eTestNames:: INCONSISTENT_LOCUS_TAG_PREFIX , "INCONSISTENT_LOCUS_TAG_PREFIX" , "Inconsistent locus tag prefix" , eDisc | eSubmitter | eSmart , nullptr }
staticconstexpr

Definition at line 796 of file discrepancy_case.cpp.

◆ s_testcase_props_INCONSISTENT_MOLTYPES

constexpr CDiscrepancyCaseProps s_testcase_props_INCONSISTENT_MOLTYPES = { CDiscrepancyVisitorImpl<eTestNames:: INCONSISTENT_MOLTYPES >::Create, eTestTypes:: SEQUENCE , eTestNames:: INCONSISTENT_MOLTYPES , "INCONSISTENT_MOLTYPES" , "Inconsistent molecule types" , eDisc | eOncaller | eSmart , nullptr }
staticconstexpr

Definition at line 837 of file discrepancy_case.cpp.

◆ s_testcase_props_INCONSISTENT_PROTEIN_ID

constexpr CDiscrepancyCaseProps s_testcase_props_INCONSISTENT_PROTEIN_ID = { CDiscrepancyVisitorImpl<eTestNames:: INCONSISTENT_PROTEIN_ID >::Create, eTestTypes:: SEQUENCE , eTestNames:: INCONSISTENT_PROTEIN_ID , "INCONSISTENT_PROTEIN_ID" , "Inconsistent Protein ID" , eDisc | eSubmitter | eSmart | eFatal , nullptr }
staticconstexpr

Definition at line 115 of file discrepancy_case.cpp.

◆ s_testcase_props_INTERNAL_TRANSCRIBED_SPACER_RRNA

constexpr CDiscrepancyCaseProps s_testcase_props_INTERNAL_TRANSCRIBED_SPACER_RRNA = { CDiscrepancyVisitorImpl<eTestNames:: INTERNAL_TRANSCRIBED_SPACER_RRNA >::Create, eTestTypes:: FEAT , eTestNames:: INTERNAL_TRANSCRIBED_SPACER_RRNA , "INTERNAL_TRANSCRIBED_SPACER_RRNA" , "Look for rRNAs that contain either 'internal', 'transcribed' or 'spacer'" , eOncaller , nullptr }
staticconstexpr

Definition at line 202 of file discrepancy_case.cpp.

◆ s_testcase_props_LONG_NO_ANNOTATION

constexpr CDiscrepancyCaseProps s_testcase_props_LONG_NO_ANNOTATION = { CDiscrepancyVisitorImpl<eTestNames:: LONG_NO_ANNOTATION >::Create, eTestTypes:: SEQUENCE , eTestNames:: LONG_NO_ANNOTATION , "LONG_NO_ANNOTATION" , "No annotation for LONG sequence" , eDisc | eOncaller | eSubmitter | eSmart | eBig , nullptr }
staticconstexpr

Definition at line 601 of file discrepancy_case.cpp.

◆ s_testcase_props_MISSING_LOCUS_TAGS

constexpr CDiscrepancyCaseProps s_testcase_props_MISSING_LOCUS_TAGS = { CDiscrepancyVisitorImpl<eTestNames:: MISSING_LOCUS_TAGS >::Create, eTestTypes:: SEQUENCE , eTestNames:: MISSING_LOCUS_TAGS , "MISSING_LOCUS_TAGS" , "Missing locus tags" , eDisc | eSubmitter | eSmart | eFatal , nullptr }
staticconstexpr

Definition at line 737 of file discrepancy_case.cpp.

◆ s_testcase_props_MISSING_PROTEIN_ID

constexpr CDiscrepancyCaseProps s_testcase_props_MISSING_PROTEIN_ID = { CDiscrepancyVisitorImpl<eTestNames:: MISSING_PROTEIN_ID >::Create, eTestTypes:: SEQUENCE , eTestNames:: MISSING_PROTEIN_ID , "MISSING_PROTEIN_ID" , "Missing Protein ID" , eDisc | eSubmitter | eSmart | eFatal , nullptr }
staticconstexpr

Definition at line 105 of file discrepancy_case.cpp.

◆ s_testcase_props_N_RUNS

constexpr CDiscrepancyCaseProps s_testcase_props_N_RUNS = { CDiscrepancyVisitorImpl<eTestNames:: N_RUNS >::Create, eTestTypes:: SEQUENCE , eTestNames:: N_RUNS , "N_RUNS" , "More than 10 Ns in a row" , eDisc | eSubmitter | eSmart | eBig | eFatal , nullptr }
staticconstexpr

Definition at line 167 of file discrepancy_case.cpp.

◆ s_testcase_props_NO_ANNOTATION

constexpr CDiscrepancyCaseProps s_testcase_props_NO_ANNOTATION = { CDiscrepancyVisitorImpl<eTestNames:: NO_ANNOTATION >::Create, eTestTypes:: SEQUENCE , eTestNames:: NO_ANNOTATION , "NO_ANNOTATION" , "No annotation" , eDisc | eOncaller | eSubmitter | eSmart | eBig , nullptr }
staticconstexpr

Definition at line 592 of file discrepancy_case.cpp.

◆ s_testcase_props_NO_LOCUS_TAGS

constexpr CDiscrepancyCaseProps s_testcase_props_NO_LOCUS_TAGS = { CDiscrepancyVisitorImpl<eTestNames:: NO_LOCUS_TAGS >::Create, eTestTypes:: FEAT , eTestNames:: NO_LOCUS_TAGS , "NO_LOCUS_TAGS" , "No locus tags at all" , eDisc | eSubmitter | eSmart | eFatal , nullptr }
staticconstexpr

Definition at line 767 of file discrepancy_case.cpp.

◆ s_testcase_props_NONWGS_SETS_PRESENT

constexpr CDiscrepancyCaseProps s_testcase_props_NONWGS_SETS_PRESENT = { CDiscrepancyVisitorImpl<eTestNames:: NONWGS_SETS_PRESENT >::Create, eTestTypes:: SEQ_SET , eTestNames:: NONWGS_SETS_PRESENT , "NONWGS_SETS_PRESENT" , "Eco, mut, phy or pop sets present" , eDisc , nullptr }
staticconstexpr

Definition at line 560 of file discrepancy_case.cpp.

◆ s_testcase_props_ORDERED_LOCATION

constexpr CDiscrepancyCaseProps s_testcase_props_ORDERED_LOCATION = { CDiscrepancyVisitorImpl<eTestNames:: ORDERED_LOCATION >::Create, eTestTypes:: FEAT , eTestNames:: ORDERED_LOCATION , "ORDERED_LOCATION" , "Location is ordered (intervals interspersed with gaps)" , eDisc | eOncaller | eSmart , nullptr }
staticconstexpr

Definition at line 695 of file discrepancy_case.cpp.

◆ s_testcase_props_OVERLAPPING_CDS

constexpr CDiscrepancyCaseProps s_testcase_props_OVERLAPPING_CDS = { CDiscrepancyVisitorImpl<eTestNames:: OVERLAPPING_CDS >::Create, eTestTypes:: SEQUENCE , eTestNames:: OVERLAPPING_CDS , "OVERLAPPING_CDS" , "Overlapping CDs" , eDisc , nullptr }
staticconstexpr

Definition at line 311 of file discrepancy_case.cpp.

◆ s_testcase_props_PARTIAL_CDS_COMPLETE_SEQUENCE

constexpr CDiscrepancyCaseProps s_testcase_props_PARTIAL_CDS_COMPLETE_SEQUENCE = { CDiscrepancyVisitorImpl<eTestNames:: PARTIAL_CDS_COMPLETE_SEQUENCE >::Create, eTestTypes:: FEAT , eTestNames:: PARTIAL_CDS_COMPLETE_SEQUENCE , "PARTIAL_CDS_COMPLETE_SEQUENCE" , "Partial CDSs in Complete Sequences" , eDisc | eOncaller | eSubmitter | eSmart , nullptr }
staticconstexpr

Definition at line 366 of file discrepancy_case.cpp.

◆ s_testcase_props_PERCENT_N

constexpr CDiscrepancyCaseProps s_testcase_props_PERCENT_N = { CDiscrepancyVisitorImpl<eTestNames:: PERCENT_N >::Create, eTestTypes:: SEQUENCE , eTestNames:: PERCENT_N , "PERCENT_N" , "More than 5 percent Ns" , eDisc | eSubmitter | eSmart | eBig , nullptr }
staticconstexpr

Definition at line 185 of file discrepancy_case.cpp.

◆ s_testcase_props_POSSIBLE_LINKER

constexpr CDiscrepancyCaseProps s_testcase_props_POSSIBLE_LINKER = { CDiscrepancyVisitorImpl<eTestNames:: POSSIBLE_LINKER >::Create, eTestTypes:: SEQUENCE , eTestNames:: POSSIBLE_LINKER , "POSSIBLE_LINKER" , "Detect linker sequence after poly-A tail" , eOncaller , nullptr }
staticconstexpr

Definition at line 629 of file discrepancy_case.cpp.

◆ s_testcase_props_QUALITY_SCORES

constexpr CDiscrepancyCaseProps s_testcase_props_QUALITY_SCORES = { CDiscrepancyVisitorImpl<eTestNames:: QUALITY_SCORES >::Create, eTestTypes:: SEQUENCE , eTestNames:: QUALITY_SCORES , "QUALITY_SCORES" , "Check for quality scores" , eDisc | eSmart , nullptr }
staticconstexpr

Definition at line 918 of file discrepancy_case.cpp.

◆ s_testcase_props_RNA_NO_PRODUCT

constexpr CDiscrepancyCaseProps s_testcase_props_RNA_NO_PRODUCT = { CDiscrepancyVisitorImpl<eTestNames:: RNA_NO_PRODUCT >::Create, eTestTypes:: FEAT , eTestNames:: RNA_NO_PRODUCT , "RNA_NO_PRODUCT" , "Find RNAs without Products" , eDisc | eOncaller | eSubmitter | eSmart , nullptr }
staticconstexpr

Definition at line 387 of file discrepancy_case.cpp.

◆ s_testcase_props_SEGSETS_PRESENT

constexpr CDiscrepancyCaseProps s_testcase_props_SEGSETS_PRESENT = { CDiscrepancyVisitorImpl<eTestNames:: SEGSETS_PRESENT >::Create, eTestTypes:: SEQ_SET , eTestNames:: SEGSETS_PRESENT , "SEGSETS_PRESENT" , "Segsets present" , eDisc | eSmart | eFatal , nullptr }
staticconstexpr

Definition at line 907 of file discrepancy_case.cpp.

◆ s_testcase_props_VERY_LONG_NO_ANNOTATION

constexpr CDiscrepancyCaseProps s_testcase_props_VERY_LONG_NO_ANNOTATION = { CDiscrepancyVisitorImpl<eTestNames:: VERY_LONG_NO_ANNOTATION >::Create, eTestTypes:: SEQUENCE , eTestNames:: VERY_LONG_NO_ANNOTATION , "VERY_LONG_NO_ANNOTATION" , "No annotation for LONG sequence" , eDisc | eOncaller | eSubmitter | eSmart | eBig , nullptr }
staticconstexpr

Definition at line 614 of file discrepancy_case.cpp.

◆ s_testcase_props_ZERO_BASECOUNT

constexpr CDiscrepancyCaseProps s_testcase_props_ZERO_BASECOUNT = { CDiscrepancyVisitorImpl<eTestNames:: ZERO_BASECOUNT >::Create, eTestTypes:: SEQUENCE , eTestNames:: ZERO_BASECOUNT , "ZERO_BASECOUNT" , "Zero Base Counts" , eDisc | eOncaller | eSubmitter | eSmart | eBig , nullptr }
staticconstexpr

Definition at line 534 of file discrepancy_case.cpp.

Modified on Tue Apr 16 20:12:37 2024 by modify_doxy.py rev. 669887