diff --git a/stxtyper.cpp b/stxtyper.cpp index 08ea111..81649b0 100644 --- a/stxtyper.cpp +++ b/stxtyper.cpp @@ -32,7 +32,7 @@ * Dependencies: NCBI BLAST, gunzip (optional) * * Release changes: -* 1.0.16 03/13/2024 PD-4926 --amrfinder: _operon, "Gene symbol" -> "Element symbol" +* 1.0.16 03/13/2024 PD-4926 --amrfinder: _operon, "Gene symbol" -> "Element symbol" * 1.0.15 03/11/2024 PD-4924 dead stxA2j EFK5907329.1 is replaced by EMA1832120.1 * 1.0.14 03/05/2024 PD-4918 --print_node: print AMRFinderPlus hierarchy node * 1.0.13 03/05/2024 PD-4910 --amrfinder prints output in the AMRFinderPlus format @@ -252,14 +252,14 @@ struct BlastAlignment << targetStart + 1 // 3 "Start" << targetEnd // 4 "Stop" << strand // 5 "Strand" - << stxType_reported // 6 "Gene symbol" + << stxType_reported + "_operon" // 6 "Gene symbol" << "Shiga toxin" // 7 "Sequence name" << "plus" // 8 "Scope" << "VIRULENCE" // 9 "Element type" << "VIRULENCE" //10 "Element subtype" << subclass. substr (0, 4) //11 "Class" << subclass //12 "Subclass" - << operon + "_operon" //13 "Method" // PD-4926 + << operon //13 "Method" << targetAlign_aa //14 "Target length" << refLen //15 "Reference sequence length" << refCoverage //16 "% Coverage of reference sequence" @@ -506,14 +506,14 @@ struct Operon << start // 3 "Start" << stop // 4 "Stop" << strand // 5 "Strand" - << stxType_reported // 6 "Gene symbol" + << stxType_reported + "_operon" // 6 "Gene symbol" << "Shiga toxin" // 7 "Sequence name" << "plus" // 8 "Scope" << "VIRULENCE" // 9 "Element type" << "VIRULENCE" //10 "Element subtype" << subclass. substr (0, 4) //11 "Class" << subclass //12 "Subclass" - << operonType + "_operon" //13 "Method" // PD-4926 + << operonType //13 "Method" << targetLen //14 "Target length" << refLen //15 "Reference sequence length" << refCoverage //16 "% Coverage of reference sequence"