diff --git a/amr_report.cpp b/amr_report.cpp index f968c52..0b79949 100644 --- a/amr_report.cpp +++ b/amr_report.cpp @@ -838,7 +838,7 @@ struct BlastAlignment : Alignment return getGeneSymbol (); string s; for (const BlastAlignment* fusion : fusions) - add (s, "/", fusion->getGeneSymbol ()); + add (s, "/" /*fusion_infix*/, fusion->getGeneSymbol ()); // PD-5155 ?? return s; } string fusion2famIds () const @@ -846,7 +846,7 @@ struct BlastAlignment : Alignment return famId; string s; for (const BlastAlignment* fusion : fusions) - add (s, "/", fusion->famId); + add (s, fusion_infix, fusion->famId); return s; } private: diff --git a/amrfinder.cpp b/amrfinder.cpp index 7d6d95b..dd876de 100644 --- a/amrfinder.cpp +++ b/amrfinder.cpp @@ -33,6 +33,9 @@ * Dependencies: NCBI BLAST, HMMer, libcurl, gunzip (optional) * * Release changes: +* 4.0.1 10/22/2024 PD-5155 "::" as a fusion infix for hierarchy_node +* PD-5085 Change column "Element length" to "Target length" +* PD-5085 StxTyper version 1.0.26 * 4.0.0 10/22/2024 PD-5156 StxTyper etc. * 3.13.3 09/11/2024 Instruction for -gff: "Locations are in the --nucleotide file." * StxTyper version 1.0.25 @@ -330,7 +333,7 @@ using namespace GFF_sp; const string dataVer_min ("2024-08-14.2"); // 3.12: "2023-12-15.2" // 3.11: "2021-02-18.1" -const string stxTyperVersion ("1.0.25"); +const string stxTyperVersion ("1.0.26"); diff --git a/columns.hpp b/columns.hpp index 4bce600..cf25a92 100644 --- a/columns.hpp +++ b/columns.hpp @@ -52,7 +52,7 @@ constexpr const char* class_colName = "Class"; constexpr const char* subclass_colName = "Subclass"; // constexpr const char* method_colName = "Method"; -constexpr const char* targetLen_colName = "Element length"; // was: "Target length" ?? +constexpr const char* targetLen_colName = "Target length"; // was: "Element length" (temporarily) constexpr const char* refLen_colName = "Reference sequence length"; constexpr const char* refCov_colName = "% Coverage of reference"; constexpr const char* refIdent_colName = "% Identity to reference"; @@ -62,3 +62,8 @@ constexpr const char* closestRefName_colName = "Closest reference name"; constexpr const char* hmmAccession_colName = "HMM accession"; constexpr const char* hmmDescr_colName = "HMM description"; constexpr const char* hierarchyNode_colName = "Hierarchy node"; + + +// PD-5155 +constexpr const char* fusion_infix = "::"; // was: "/" + \ No newline at end of file diff --git a/stxtyper b/stxtyper index 94ac374..b845df0 160000 --- a/stxtyper +++ b/stxtyper @@ -1 +1 @@ -Subproject commit 94ac374d0eca8e6d97d198c1db8cf26baa0c785c +Subproject commit b845df0808194a834471b382ae2b7c263024d009 diff --git a/version.txt b/version.txt index fcdb2e1..1454f6e 100644 --- a/version.txt +++ b/version.txt @@ -1 +1 @@ -4.0.0 +4.0.1