diff --git a/amrfinder_columns.hpp b/amrfinder_columns.hpp index cf25a92..4d5b1a3 100644 --- a/amrfinder_columns.hpp +++ b/amrfinder_columns.hpp @@ -66,4 +66,5 @@ constexpr const char* hierarchyNode_colName = "Hierarchy node"; // PD-5155 constexpr const char* fusion_infix = "::"; // was: "/" - \ No newline at end of file + +constexpr const char* na ("NA"); diff --git a/stxtyper.cpp b/stxtyper.cpp index 2982f48..1b6f5fd 100644 --- a/stxtyper.cpp +++ b/stxtyper.cpp @@ -32,6 +32,7 @@ * Dependencies: NCBI BLAST, gunzip (optional) * * Release changes: +* 1.0.32 12/20/2024 PD-5201 Change empty fields to NA * 1.0.31 12/17/2024 PD-5181 COMPLETE and COMPLETE_NOVEL is preferred over the other operon types * operons with higher identity and higher coverage are preferred * 1.0.30 12/14/2024 Bug in --debug @@ -129,7 +130,7 @@ constexpr size_t slack = 30; constexpr double identity_min = 0.8; // PD-5192 const string stxS ("stx"); -const string na ("NA"); +//const string na ("NA"); @@ -351,8 +352,8 @@ struct BlastAlignment << subclass //12 "Subclass" << quality //13 "Method" << targetEnd - targetStart /*targetAlign*/ //14 "Target length" - << noString /*refLen*/ //15 "Reference sequence length" - << noString /*refCoverage*/ //16 "% Coverage of reference sequence" + << na /*refLen*/ //15 "Reference sequence length" + << na /*refCoverage*/ //16 "% Coverage of reference sequence" << refIdentity //17 "% Identity to reference sequence" << length //18 "Alignment length" << refAccession //19 "Accession of closest sequence" @@ -368,24 +369,24 @@ struct BlastAlignment td << targetName << stxType_reported << quality - << noString + << na << targetStart + 1 << targetEnd << strand; if (subunit == 'B') - td << noString - << noString - << noString - << noString; + td << na + << na + << na + << na; td << refAccession << subClass << refIdentity << refCoverage; if (subunit == 'A') - td << noString - << noString - << noString - << noString; + td << na + << na + << na + << na; } td. newLn (); } @@ -608,6 +609,7 @@ struct Operon : al1->partial () || al2->partial () ? "PARTIAL" + // complete operon types : novel ? ambig () ? "AMBIGUOUS" @@ -656,8 +658,8 @@ struct Operon << subclass //12 "Subclass" << quality //13 "Method" << targetAlign //14 "Target length" - << noString /*refLen*/ //15 "Reference sequence length" - << noString /*refCoverage*/ //16 "% Coverage of reference sequence" + << na /*refLen*/ //15 "Reference sequence length" + << na /*refCoverage*/ //16 "% Coverage of reference sequence" << refIdentity //17 "% Identity to reference sequence" << alignmentLen //18 "Alignment length" << refAccessions //19 "Accession of closest sequence" @@ -945,7 +947,7 @@ struct ThisApplication final : ShellApplication stderr << "Version: " << version << '\n'; const string logFName (tmp + "/log"); - const string qcS (qc_on ? " -qc" : ""); + const string qcS (qc_on ? " -qc" : noString); // blast_bin diff --git a/version.txt b/version.txt index 9495615..15245f3 100644 --- a/version.txt +++ b/version.txt @@ -1 +1 @@ -1.0.31 +1.0.32