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NCBI C++ ToolKit: src/misc/discrepancy/sequence_tests.cpp File Reference

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  USING_SCOPE (objects)   static bool  IsATGC (char ch)   static bool  EndsWithSequence (const string &title)   string  GetFieldValueAsString (const CUser_field &field)   void  AddUserObjectFieldItems (const CSeqdesc *desc, CReportObj &rep_seq, CReportNode &collector, CReportNode &previously_seen, CDiscrepancyContext &context, const string &object_name, const string &field_prefix=kEmptyStr)   void  AnalyzeField (CReportNode &node, bool &all_present, bool &all_same)   void  AnalyzeFieldReport (CReportNode &node, bool &all_present, bool &all_same)   string  GetSummaryLabel (bool all_present, bool all_same)   void  CopyNode (CReportNode &new_home, CReportNode &original)   string  AdjustDBLinkFieldName (const string &orig_field_name)   static string  GetProjectID (const CUser_object &user)   static bool  IsMolProd (int biomol)   static bool  CompareOrGetString (const CBioSource &bio_src, FnIsSet is_set_fn, FnGet get_fn, string &val)   static bool  CompareOrgModValue (const CBioSource &bio_src, COrgMod::TSubtype subtype, string &val)   static bool  IsSegmentSubtype (const CBioSource &bio_src)   static bool  IsMicroSatellite (const CSeq_feat &feat)   static void  FindFlatfileText (const char *str, bool *result)   void  UnitTest_FLATFILE_FIND ()   Checking that FLATFILE_FIND.inc is in sync with kSpellFixes If the array is changed, need to regenerate FLATFILE_FIND.inc: multipattern.exe -i FLATFILE_FIND.txt > FLATFILE_FIND.inc. More...
  static bool  FixTextInObject (CSerialObject *obj, size_t misspell_idx)   static bool  SuspiciousId (const string &s)   static bool  s_areCompatible (CBioSource::EGenome Location, CSubSource::ESubtype Qualifier)   const string  kUniqueDeflines = "[n] definition line[s] [is] unique"   const string  kIdenticalDeflines = "[n] definition line[s] [is] identical"   const string  kAllUniqueDeflines = "All deflines are unique"   const string  kSomeIdenticalDeflines = "Defline Problem Report"   static constexpr CDiscrepancyCaseProps  s_testcase_props_DUP_DEFLINE = { CDiscrepancyVisitorImpl<eTestNames:: DUP_DEFLINE >::Create, eTestTypes:: SEQUENCE , eTestNames:: DUP_DEFLINE , "DUP_DEFLINE" , "Definition lines should be unique" , eOncaller , nullptr }   static constexpr CDiscrepancyCaseProps  s_testcase_props_TERMINAL_NS = { CDiscrepancyVisitorImpl<eTestNames:: TERMINAL_NS >::Create, eTestTypes:: SEQUENCE , eTestNames:: TERMINAL_NS , "TERMINAL_NS" , "Ns at end of sequences" , eDisc | eSmart | eBig | eFatal , nullptr }   static constexpr CDiscrepancyCaseProps  s_testcase_props_SHORT_PROT_SEQUENCES = { CDiscrepancyVisitorImpl<eTestNames:: SHORT_PROT_SEQUENCES >::Create, eTestTypes:: SEQUENCE , eTestNames:: SHORT_PROT_SEQUENCES , "SHORT_PROT_SEQUENCES" , "Protein sequences should be at least 50 aa, unless they are partial" , eDisc | eOncaller | eSmart , nullptr }   static constexpr CDiscrepancyCaseProps  s_testcase_props_COMMENT_PRESENT = { CDiscrepancyVisitorImpl<eTestNames:: COMMENT_PRESENT >::Create, eTestTypes:: DESC , eTestNames:: COMMENT_PRESENT , "COMMENT_PRESENT" , "Comment descriptor present" , eOncaller , nullptr }   static constexpr CDiscrepancyCaseProps  s_testcase_props_MRNA_ON_WRONG_SEQUENCE_TYPE = { CDiscrepancyVisitorImpl<eTestNames:: MRNA_ON_WRONG_SEQUENCE_TYPE >::Create, eTestTypes:: SEQUENCE , eTestNames:: MRNA_ON_WRONG_SEQUENCE_TYPE , "MRNA_ON_WRONG_SEQUENCE_TYPE" , "Eukaryotic sequences that are not genomic or macronuclear should not have mRNA features" , eDisc | eOncaller , nullptr }   const string  kSequencesWithGaps = "[n] sequence[s] contain[S] gaps"   static constexpr CDiscrepancyCaseProps  s_testcase_props_GAPS = { CDiscrepancyVisitorImpl<eTestNames:: GAPS >::Create, eTestTypes:: SEQUENCE , eTestNames:: GAPS , "GAPS" , "Sequences with gaps" , eDisc | eSubmitter | eSmart | eBig , nullptr }   static constexpr CDiscrepancyCaseProps  s_testcase_props_BIOPROJECT_ID = { CDiscrepancyVisitorImpl<eTestNames:: BIOPROJECT_ID >::Create, eTestTypes:: SEQUENCE , eTestNames:: BIOPROJECT_ID , "BIOPROJECT_ID" , "Sequences with BioProject IDs" , eOncaller , nullptr }   static constexpr CDiscrepancyCaseProps  s_testcase_props_SEQUENCE_READ_ARCHIVE = { CDiscrepancyVisitorImpl<eTestNames:: SEQUENCE_READ_ARCHIVE >::Create, eTestTypes:: SEQUENCE , eTestNames:: SEQUENCE_READ_ARCHIVE , "SEQUENCE_READ_ARCHIVE" , "Sequences with Sequence Read Archive IDs" , eSubmitter | eSmart , nullptr }   static constexpr CDiscrepancyCaseProps  s_testcase_props_MISSING_DEFLINES = { CDiscrepancyVisitorImpl<eTestNames:: MISSING_DEFLINES >::Create, eTestTypes:: SEQUENCE , eTestNames:: MISSING_DEFLINES , "MISSING_DEFLINES" , "Missing definition lines" , eAll , nullptr }   static constexpr CDiscrepancyCaseProps  s_testcase_props_N_RUNS_14 = { CDiscrepancyVisitorImpl<eTestNames:: N_RUNS_14 >::Create, eTestTypes:: SEQUENCE , eTestNames:: N_RUNS_14 , "N_RUNS_14" , "Runs of more than 14 Ns" , eDisc | eTSA , nullptr }   static constexpr CDiscrepancyCaseProps  s_testcase_props_EXTERNAL_REFERENCE = { CDiscrepancyVisitorImpl<eTestNames:: EXTERNAL_REFERENCE >::Create, eTestTypes:: SEQUENCE , eTestNames:: EXTERNAL_REFERENCE , "EXTERNAL_REFERENCE" , "Sequence has external reference" , eDisc | eOncaller , nullptr }   static constexpr CDiscrepancyCaseProps  s_testcase_props_TEN_PERCENTN = { CDiscrepancyVisitorImpl<eTestNames:: TEN_PERCENTN >::Create, eTestTypes:: SEQUENCE , eTestNames:: TEN_PERCENTN , "10_PERCENTN" , "Greater than 10 percent Ns" , eDisc | eSubmitter | eSmart | eTSA , nullptr }   static constexpr CDiscrepancyCaseProps  s_testcase_props_FEATURE_COUNT = { CDiscrepancyVisitorImpl<eTestNames:: FEATURE_COUNT >::Create, eTestTypes:: FEAT , eTestNames:: FEATURE_COUNT , "FEATURE_COUNT" , "Count features present or missing from sequences" , eOncaller | eSubmitter | eSmart , nullptr }   static constexpr CDiscrepancyCaseProps  s_testcase_props_EXON_ON_MRNA = { CDiscrepancyVisitorImpl<eTestNames:: EXON_ON_MRNA >::Create, eTestTypes:: SEQUENCE , eTestNames:: EXON_ON_MRNA , "EXON_ON_MRNA" , "mRNA sequences should not have exons" , eOncaller | eSmart , nullptr }   static constexpr CDiscrepancyCaseProps  s_testcase_props_INCONSISTENT_MOLINFO_TECH = { CDiscrepancyVisitorImpl<eTestNames:: INCONSISTENT_MOLINFO_TECH >::Create, eTestTypes:: SEQUENCE , eTestNames:: INCONSISTENT_MOLINFO_TECH , "INCONSISTENT_MOLINFO_TECH" , "Inconsistent Molinfo Techniques" , eDisc | eSmart , nullptr }   static const string  kInconsistentMolinfoTechSummary = "Molinfo Technique Report"   static const string  kInconsistentMolinfoTech = "[n] Molinfo[s] [is] missing field technique"   static constexpr CDiscrepancyCaseProps  s_testcase_props_TITLE_ENDS_WITH_SEQUENCE = { CDiscrepancyVisitorImpl<eTestNames:: TITLE_ENDS_WITH_SEQUENCE >::Create, eTestTypes:: DESC , eTestNames:: TITLE_ENDS_WITH_SEQUENCE , "TITLE_ENDS_WITH_SEQUENCE" , "Sequence characters at end of defline" , eDisc | eSubmitter | eSmart | eBig , nullptr }   static constexpr CDiscrepancyCaseProps  s_testcase_props_FEATURE_MOLTYPE_MISMATCH = { CDiscrepancyVisitorImpl<eTestNames:: FEATURE_MOLTYPE_MISMATCH >::Create, eTestTypes:: SEQUENCE , eTestNames:: FEATURE_MOLTYPE_MISMATCH , "FEATURE_MOLTYPE_MISMATCH" , "Sequences with rRNA or misc_RNA features should be genomic DNA" , eOncaller , nullptr }   const string  kMissingDBLink = "[n] Bioseq [is] missing DBLink object"   const string  kDBLinkObjectList = "DBLink Objects"   const string  kDBLinkFieldCountTop = "DBLink Fields"   const string  kDBLinkCollect = "DBLink Collection"   const string &  kPreviouslySeenFields = "Previously Seen Fields"   const string &  kPreviouslySeenFieldsThis = "Previously Seen Fields This"   const string &  kPreviouslySeenObjects = "Previously Seen Objects"   static constexpr CDiscrepancyCaseProps  s_testcase_props_INCONSISTENT_DBLINK = { CDiscrepancyVisitorImpl<eTestNames:: INCONSISTENT_DBLINK >::Create, eTestTypes:: SEQUENCE , eTestNames:: INCONSISTENT_DBLINK , "INCONSISTENT_DBLINK" , "Inconsistent DBLink fields" , eDisc | eSubmitter | eSmart | eBig , nullptr }   const string  kStructuredCommentsSeqs = "sequences"   const string  kStructuredCommentObservedPrefixes = "observed prefixes"   const string  kStructuredCommentObservedPrefixesThis = "observed prefixes this"   const string  kStructuredCommentReport = "collection"   const string  kStructuredCommentPrevious = "previous"   const string  kStructuredCommentFieldPrefix = "structured comment field "   static constexpr CDiscrepancyCaseProps  s_testcase_props_INCONSISTENT_STRUCTURED_COMMENTS = { CDiscrepancyVisitorImpl<eTestNames:: INCONSISTENT_STRUCTURED_COMMENTS >::Create, eTestTypes:: SEQUENCE , eTestNames:: INCONSISTENT_STRUCTURED_COMMENTS , "INCONSISTENT_STRUCTURED_COMMENTS" , "Inconsistent structured comments" , eDisc | eSubmitter | eSmart | eBig , nullptr }   static constexpr CDiscrepancyCaseProps  s_testcase_props_ASSEMBLY_NAME_IN_GENOME_ASSEMBLY = { CDiscrepancyVisitorImpl<eTestNames:: ASSEMBLY_NAME_IN_GENOME_ASSEMBLY >::Create, eTestTypes:: SEQUENCE , eTestNames:: ASSEMBLY_NAME_IN_GENOME_ASSEMBLY , "ASSEMBLY_NAME_IN_GENOME_ASSEMBLY" , "Assembly name in genome assembly structured comments" , eDisc | eSubmitter | eSmart , nullptr }   static constexpr CDiscrepancyCaseProps  s_testcase_props_MISSING_STRUCTURED_COMMENT = { CDiscrepancyVisitorImpl<eTestNames:: MISSING_STRUCTURED_COMMENT >::Create, eTestTypes:: SEQUENCE , eTestNames:: MISSING_STRUCTURED_COMMENT , "MISSING_STRUCTURED_COMMENT" , "Structured comment not included" , eDisc | eTSA , nullptr }   static constexpr CDiscrepancyCaseProps  s_testcase_props_MISSING_PROJECT = { CDiscrepancyVisitorImpl<eTestNames:: MISSING_PROJECT >::Create, eTestTypes:: SEQUENCE , eTestNames:: MISSING_PROJECT , "MISSING_PROJECT" , "Project not included" , eDisc | eTSA , nullptr }   static constexpr CDiscrepancyCaseProps  s_testcase_props_COUNT_UNVERIFIED = { CDiscrepancyVisitorImpl<eTestNames:: COUNT_UNVERIFIED >::Create, eTestTypes:: SEQUENCE , eTestNames:: COUNT_UNVERIFIED , "COUNT_UNVERIFIED" , "Count number of unverified sequences" , eOncaller , nullptr }   const string  kDeflineExists = "[n] Bioseq[s] [has] definition line"   static constexpr CDiscrepancyCaseProps  s_testcase_props_DEFLINE_PRESENT = { CDiscrepancyVisitorImpl<eTestNames:: DEFLINE_PRESENT >::Create, eTestTypes:: SEQUENCE , eTestNames:: DEFLINE_PRESENT , "DEFLINE_PRESENT" , "Test defline existence" , eDisc , nullptr }   static constexpr CDiscrepancyCaseProps  s_testcase_props_UNUSUAL_NT = { CDiscrepancyVisitorImpl<eTestNames:: UNUSUAL_NT >::Create, eTestTypes:: SEQUENCE , eTestNames:: UNUSUAL_NT , "UNUSUAL_NT" , "Sequence contains unusual nucleotides" , eDisc | eSubmitter | eSmart , nullptr }   const string  kNoTaxnameInDefline = "[n] defline[s] [does] not contain the complete taxname"   static constexpr CDiscrepancyCaseProps  s_testcase_props_TAXNAME_NOT_IN_DEFLINE = { CDiscrepancyVisitorImpl<eTestNames:: TAXNAME_NOT_IN_DEFLINE >::Create, eTestTypes:: SEQUENCE , eTestNames:: TAXNAME_NOT_IN_DEFLINE , "TAXNAME_NOT_IN_DEFLINE" , "Complete taxname should be present in definition line" , eDisc | eOncaller , nullptr }   static constexpr CDiscrepancyCaseProps  s_testcase_props_HAS_PROJECT_ID = { CDiscrepancyVisitorImpl<eTestNames:: HAS_PROJECT_ID >::Create, eTestTypes:: SEQUENCE , eTestNames:: HAS_PROJECT_ID , "HAS_PROJECT_ID" , "Sequences with project IDs (looks for genome project IDs)" , eOncaller | eSmart , nullptr }   static constexpr CDiscrepancyCaseProps  s_testcase_props_MULTIPLE_CDS_ON_MRNA = { CDiscrepancyVisitorImpl<eTestNames:: MULTIPLE_CDS_ON_MRNA >::Create, eTestTypes:: SEQUENCE , eTestNames:: MULTIPLE_CDS_ON_MRNA , "MULTIPLE_CDS_ON_MRNA" , "Multiple CDS on mRNA" , eOncaller | eSubmitter | eSmart , nullptr }   static const string  kMrnaSequenceMinusStrandFeatures = "[n] mRNA sequences have features on the complement strand."   static constexpr CDiscrepancyCaseProps  s_testcase_props_MRNA_SEQUENCE_MINUS_STRAND_FEATURES = { CDiscrepancyVisitorImpl<eTestNames:: MRNA_SEQUENCE_MINUS_STRAND_FEATURES >::Create, eTestTypes:: SEQUENCE , eTestNames:: MRNA_SEQUENCE_MINUS_STRAND_FEATURES , "MRNA_SEQUENCE_MINUS_STRAND_FEATURES" , "mRNA sequences have CDS/gene on the complement strand" , eOncaller , nullptr }   static constexpr CDiscrepancyCaseProps  s_testcase_props_LOW_QUALITY_REGION = { CDiscrepancyVisitorImpl<eTestNames:: LOW_QUALITY_REGION >::Create, eTestTypes:: SEQUENCE , eTestNames:: LOW_QUALITY_REGION , "LOW_QUALITY_REGION" , "Sequence contains regions of low quality" , eDisc | eSubmitter | eSmart , nullptr }   static constexpr CDiscrepancyCaseProps  s_testcase_props_DEFLINE_ON_SET = { CDiscrepancyVisitorImpl<eTestNames:: DEFLINE_ON_SET >::Create, eTestTypes:: SEQ_SET , eTestNames:: DEFLINE_ON_SET , "DEFLINE_ON_SET" , "Titles on sets" , eOncaller , nullptr }   static constexpr CDiscrepancyCaseProps  s_testcase_props_MITOCHONDRION_REQUIRED = { CDiscrepancyVisitorImpl<eTestNames:: MITOCHONDRION_REQUIRED >::Create, eTestTypes:: SEQUENCE , eTestNames:: MITOCHONDRION_REQUIRED , "MITOCHONDRION_REQUIRED" , "If D-loop or control region misc_feat is present, source must be mitochondrial" , eDisc | eOncaller , nullptr }   static constexpr CDiscrepancyCaseProps  s_testcase_props_SEQ_SHORTER_THAN_50bp = { CDiscrepancyVisitorImpl<eTestNames:: SEQ_SHORTER_THAN_50bp >::Create, eTestTypes:: SEQUENCE , eTestNames:: SEQ_SHORTER_THAN_50bp , "SEQ_SHORTER_THAN_50bp" , "Find Short Sequences" , eDisc | eSubmitter | eSmart | eBig , nullptr }   static constexpr CDiscrepancyCaseProps  s_testcase_props_SEQ_SHORTER_THAN_200bp = { CDiscrepancyVisitorImpl<eTestNames:: SEQ_SHORTER_THAN_200bp >::Create, eTestTypes:: SEQUENCE , eTestNames:: SEQ_SHORTER_THAN_200bp , "SEQ_SHORTER_THAN_200bp" , "Short Contig" , eDisc | eSubmitter | eSmart | eBig | eTSA , nullptr }   static constexpr CDiscrepancyCaseProps  s_testcase_props_RNA_PROVIRAL = { CDiscrepancyVisitorImpl<eTestNames:: RNA_PROVIRAL >::Create, eTestTypes:: SEQUENCE , eTestNames:: RNA_PROVIRAL , "RNA_PROVIRAL" , "RNA bioseqs are proviral" , eOncaller , nullptr }   static constexpr CDiscrepancyCaseProps  s_testcase_props_SMALL_GENOME_SET_PROBLEM = { CDiscrepancyVisitorImpl<eTestNames:: SMALL_GENOME_SET_PROBLEM >::Create, eTestTypes:: SEQ_SET , eTestNames:: SMALL_GENOME_SET_PROBLEM , "SMALL_GENOME_SET_PROBLEM" , "Problems with small genome sets" , eOncaller , nullptr }   static constexpr CDiscrepancyCaseProps  s_testcase_props_UNWANTED_SET_WRAPPER = { CDiscrepancyVisitorImpl<eTestNames:: UNWANTED_SET_WRAPPER >::Create, eTestTypes:: FEAT , eTestNames:: UNWANTED_SET_WRAPPER , "UNWANTED_SET_WRAPPER" , "Set wrapper on microsatellites or rearranged genes" , eOncaller , nullptr }   static constexpr auto  kSpellFixes   static constexpr size_t  kSpellFixesSize = kSpellFixes.size()   static constexpr std::initializer_list< const char * >  g_aliases_FLATFILE_FIND = { "FLATFILE_FIND_ONCALLER", "FLATFILE_FIND_ONCALLER_UNFIXABLE", "FLATFILE_FIND_ONCALLER_FIXABLE" }   static constexpr CDiscrepancyCaseProps  s_testcase_props_FLATFILE_FIND = { CDiscrepancyVisitorImpl<eTestNames:: FLATFILE_FIND >::Create, eTestTypes:: SEQUENCE , eTestNames:: FLATFILE_FIND , "FLATFILE_FIND" , "Flatfile representation of object contains suspect text" , eOncaller , &g_aliases_FLATFILE_FIND }   static const size_t  MIN_SEQUENCE_LEN = 20000   static constexpr CDiscrepancyCaseProps  s_testcase_props_ALL_SEQS_SHORTER_THAN_20kb = { CDiscrepancyVisitorImpl<eTestNames:: ALL_SEQS_SHORTER_THAN_20kb >::Create, eTestTypes:: SEQUENCE , eTestNames:: ALL_SEQS_SHORTER_THAN_20kb , "ALL_SEQS_SHORTER_THAN_20kb" , "Short sequences test" , eDisc | eSubmitter | eSmart | eBig , nullptr }   static constexpr CDiscrepancyCaseProps  s_testcase_props_ALL_SEQS_CIRCULAR = { CDiscrepancyVisitorImpl<eTestNames:: ALL_SEQS_CIRCULAR >::Create, eTestTypes:: SEQUENCE , eTestNames:: ALL_SEQS_CIRCULAR , "ALL_SEQS_CIRCULAR" , "All sequences circular" , eDisc | eSubmitter | eSmart , nullptr }   static constexpr CDiscrepancyCaseProps  s_testcase_props_SUSPICIOUS_SEQUENCE_ID = { CDiscrepancyVisitorImpl<eTestNames:: SUSPICIOUS_SEQUENCE_ID >::Create, eTestTypes:: SEQUENCE , eTestNames:: SUSPICIOUS_SEQUENCE_ID , "SUSPICIOUS_SEQUENCE_ID" , "Suspicious sequence identifiers" , eOncaller | eSubmitter | eSmart | eBig , nullptr }   static const CSubSource::ESubtype  eSubtype_unknown = static_cast<CSubSource::ESubtype>(0)   static constexpr CDiscrepancyCaseProps  s_testcase_props_CHROMOSOME_PRESENT = { CDiscrepancyVisitorImpl<eTestNames:: CHROMOSOME_PRESENT >::Create, eTestTypes:: SEQ_SET , eTestNames:: CHROMOSOME_PRESENT , "CHROMOSOME_PRESENT" , "Chromosome present" , eSubmitter | eSmart , nullptr }   static constexpr CDiscrepancyCaseProps  s_testcase_props_ORGANELLE_PRESENT = { CDiscrepancyVisitorImpl<eTestNames:: ORGANELLE_PRESENT >::Create, eTestTypes:: SEQ_SET , eTestNames:: ORGANELLE_PRESENT , "ORGANELLE_PRESENT" , "Discrepancy present" , eSubmitter | eSmart , nullptr }   ◆ FnGet ◆ FnIsSet ◆ AddUserObjectFieldItems()

Definition at line 659 of file sequence_tests.cpp.

References CReportNode::Add(), CReportNode::clear(), context, CReportNode::Exist(), f, CUser_object_Base::GetData(), GetFieldValueAsString(), GetObjects(), CSeqdesc_Base::GetUser(), kPreviouslySeenFields, kPreviouslySeenFieldsThis, and kPreviouslySeenObjects.

◆ AdjustDBLinkFieldName() ◆ AnalyzeField() ◆ AnalyzeFieldReport() ◆ CompareOrGetString() ◆ CompareOrgModValue() ◆ CopyNode() ◆ EndsWithSequence() ◆ FindFlatfileText() ◆ FixTextInObject() ◆ GetFieldValueAsString() ◆ GetProjectID() ◆ GetSummaryLabel() ◆ IsATGC() ◆ IsMicroSatellite() ◆ IsMolProd() ◆ IsSegmentSubtype() ◆ s_areCompatible() ◆ SuspiciousId() ◆ UnitTest_FLATFILE_FIND() void UnitTest_FLATFILE_FIND ( ) ◆ USING_SCOPE() ◆ eSubtype_unknown ◆ g_aliases_FLATFILE_FIND constexpr std::initializer_list<const char*> g_aliases_FLATFILE_FIND = { "FLATFILE_FIND_ONCALLER", "FLATFILE_FIND_ONCALLER_UNFIXABLE", "FLATFILE_FIND_ONCALLER_FIXABLE" } staticconstexpr

Definition at line 1776 of file sequence_tests.cpp.

◆ kAllUniqueDeflines const string kAllUniqueDeflines = "All deflines are unique" ◆ kDBLinkCollect ◆ kDBLinkFieldCountTop ◆ kDBLinkObjectList ◆ kDeflineExists ◆ kIdenticalDeflines const string kIdenticalDeflines = "[n] definition line[s] [is] identical" ◆ kInconsistentMolinfoTech const string kInconsistentMolinfoTech = "[n] Molinfo[s] [is] missing field technique" static ◆ kInconsistentMolinfoTechSummary const string kInconsistentMolinfoTechSummary = "Molinfo Technique Report" static ◆ kMissingDBLink ◆ kMrnaSequenceMinusStrandFeatures const string kMrnaSequenceMinusStrandFeatures = "[n] mRNA sequences have features on the complement strand." static

Definition at line 1261 of file sequence_tests.cpp.

◆ kNoTaxnameInDefline ◆ kPreviouslySeenFields const string& kPreviouslySeenFields = "Previously Seen Fields" ◆ kPreviouslySeenFieldsThis const string& kPreviouslySeenFieldsThis = "Previously Seen Fields This" ◆ kPreviouslySeenObjects const string& kPreviouslySeenObjects = "Previously Seen Objects" ◆ kSequencesWithGaps ◆ kSomeIdenticalDeflines const string kSomeIdenticalDeflines = "Defline Problem Report" ◆ kSpellFixes constexpr auto kSpellFixes staticconstexpr ◆ kSpellFixesSize ◆ kStructuredCommentFieldPrefix const string kStructuredCommentFieldPrefix = "structured comment field " ◆ kStructuredCommentObservedPrefixes const string kStructuredCommentObservedPrefixes = "observed prefixes" ◆ kStructuredCommentObservedPrefixesThis const string kStructuredCommentObservedPrefixesThis = "observed prefixes this" ◆ kStructuredCommentPrevious ◆ kStructuredCommentReport ◆ kStructuredCommentsSeqs ◆ kUniqueDeflines const string kUniqueDeflines = "[n] definition line[s] [is] unique" ◆ MIN_SEQUENCE_LEN ◆ s_testcase_props_ALL_SEQS_CIRCULAR ◆ s_testcase_props_ALL_SEQS_SHORTER_THAN_20kb ◆ s_testcase_props_ASSEMBLY_NAME_IN_GENOME_ASSEMBLY ◆ s_testcase_props_BIOPROJECT_ID ◆ s_testcase_props_CHROMOSOME_PRESENT ◆ s_testcase_props_COMMENT_PRESENT ◆ s_testcase_props_COUNT_UNVERIFIED ◆ s_testcase_props_DEFLINE_ON_SET ◆ s_testcase_props_DEFLINE_PRESENT ◆ s_testcase_props_DUP_DEFLINE ◆ s_testcase_props_EXON_ON_MRNA ◆ s_testcase_props_EXTERNAL_REFERENCE ◆ s_testcase_props_FEATURE_COUNT ◆ s_testcase_props_FEATURE_MOLTYPE_MISMATCH constexpr CDiscrepancyCaseProps s_testcase_props_FEATURE_MOLTYPE_MISMATCH = { CDiscrepancyVisitorImpl<eTestNames:: FEATURE_MOLTYPE_MISMATCH >::Create, eTestTypes:: SEQUENCE , eTestNames:: FEATURE_MOLTYPE_MISMATCH , "FEATURE_MOLTYPE_MISMATCH" , "Sequences with rRNA or misc_RNA features should be genomic DNA" , eOncaller , nullptr } staticconstexpr

Definition at line 565 of file sequence_tests.cpp.

◆ s_testcase_props_FLATFILE_FIND ◆ s_testcase_props_GAPS ◆ s_testcase_props_HAS_PROJECT_ID ◆ s_testcase_props_INCONSISTENT_DBLINK ◆ s_testcase_props_INCONSISTENT_MOLINFO_TECH ◆ s_testcase_props_INCONSISTENT_STRUCTURED_COMMENTS ◆ s_testcase_props_LOW_QUALITY_REGION ◆ s_testcase_props_MISSING_DEFLINES ◆ s_testcase_props_MISSING_PROJECT ◆ s_testcase_props_MISSING_STRUCTURED_COMMENT ◆ s_testcase_props_MITOCHONDRION_REQUIRED ◆ s_testcase_props_MRNA_ON_WRONG_SEQUENCE_TYPE constexpr CDiscrepancyCaseProps s_testcase_props_MRNA_ON_WRONG_SEQUENCE_TYPE = { CDiscrepancyVisitorImpl<eTestNames:: MRNA_ON_WRONG_SEQUENCE_TYPE >::Create, eTestTypes:: SEQUENCE , eTestNames:: MRNA_ON_WRONG_SEQUENCE_TYPE , "MRNA_ON_WRONG_SEQUENCE_TYPE" , "Eukaryotic sequences that are not genomic or macronuclear should not have mRNA features" , eDisc | eOncaller , nullptr } staticconstexpr

Definition at line 186 of file sequence_tests.cpp.

◆ s_testcase_props_MRNA_SEQUENCE_MINUS_STRAND_FEATURES constexpr CDiscrepancyCaseProps s_testcase_props_MRNA_SEQUENCE_MINUS_STRAND_FEATURES = { CDiscrepancyVisitorImpl<eTestNames:: MRNA_SEQUENCE_MINUS_STRAND_FEATURES >::Create, eTestTypes:: SEQUENCE , eTestNames:: MRNA_SEQUENCE_MINUS_STRAND_FEATURES , "MRNA_SEQUENCE_MINUS_STRAND_FEATURES" , "mRNA sequences have CDS/gene on the complement strand" , eOncaller , nullptr } staticconstexpr

Definition at line 1263 of file sequence_tests.cpp.

◆ s_testcase_props_MULTIPLE_CDS_ON_MRNA ◆ s_testcase_props_N_RUNS_14 ◆ s_testcase_props_ORGANELLE_PRESENT ◆ s_testcase_props_RNA_PROVIRAL ◆ s_testcase_props_SEQ_SHORTER_THAN_200bp ◆ s_testcase_props_SEQ_SHORTER_THAN_50bp ◆ s_testcase_props_SEQUENCE_READ_ARCHIVE ◆ s_testcase_props_SHORT_PROT_SEQUENCES ◆ s_testcase_props_SMALL_GENOME_SET_PROBLEM constexpr CDiscrepancyCaseProps s_testcase_props_SMALL_GENOME_SET_PROBLEM = { CDiscrepancyVisitorImpl<eTestNames:: SMALL_GENOME_SET_PROBLEM >::Create, eTestTypes:: SEQ_SET , eTestNames:: SMALL_GENOME_SET_PROBLEM , "SMALL_GENOME_SET_PROBLEM" , "Problems with small genome sets" , eOncaller , nullptr } staticconstexpr

Definition at line 1556 of file sequence_tests.cpp.

◆ s_testcase_props_SUSPICIOUS_SEQUENCE_ID ◆ s_testcase_props_TAXNAME_NOT_IN_DEFLINE ◆ s_testcase_props_TEN_PERCENTN ◆ s_testcase_props_TERMINAL_NS ◆ s_testcase_props_TITLE_ENDS_WITH_SEQUENCE ◆ s_testcase_props_UNUSUAL_NT ◆ s_testcase_props_UNWANTED_SET_WRAPPER

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