PD-5014 duplicate susceptible proteins are not reported

amr_report.cpp

@@ -81,6 +81,7 @@ struct BlastRule : Root
  // 0 <=> undefined
  // 0 .. 1
  double ident {0.0};
+ // Of alignment
  double target_coverage {0.0}; // Not used
  double ref_coverage {0.0};
 
@@ -436,6 +437,7 @@ struct BlastAlignment : Alignment
  {
  // PD-4856
  ASSERT (! brFam);
+ // brFam
  EXEC_ASSERT (brFam = getFam ()); 
  while (brFam)
  {
@@ -1223,7 +1225,7 @@ struct BlastAlignment : Alignment
  // Requires: all SCCs of betterEq() are complete subgraphs ??
  { return betterEq (other) 
  && ( ! other. betterEq (*this)
- || (inFam () && ! equidistant && refAccession < other. refAccession) // Tie resolution: PD-1245
+ || (! isMutationProt () /*inFam () --PD-5014*/ && ! equidistant && refAccession < other. refAccession) // Tie resolution: PD-1245
  );
  }
  bool better (const HmmAlignment& other) const

amrfinder.cpp

@@ -33,6 +33,7 @@
 * Dependencies: NCBI BLAST, HMMer, libcurl, gunzip (optional)
 *
 * Release changes:
+* 3.12.21 05/31/2024 PD-5014 duplicate susceptible proteins are not reported
 * 3.12.20 05/22/2024 PD-4078 a regular reference protein can have point mutations
 * 3.12.19 05/21/2024 PD-5002 StxTyper 1.0.20
 * 05/06/2024 BlastAlignment: isMutation() => !seqChanges.empty()

tsv.cpp

@@ -51,31 +51,48 @@ namespace Common_sp
 Date Date::parse (const string &s,
  Format fmt)
 { 
- Date d;
  istringstream iss (s);
  short year = 0;
+ short month = 0;
+ short day = 0;
+ char c1 = '\0';
+ char c2 = '\0';
  string tmp;
- iss >> year >> tmp;
  switch (fmt)
  {
  case fmt_Year:
- if (! tmp. empty ())
- return d;
- if (! isYear (year))
- return d;
- return Date (year);
+ iss >> year >> tmp;
+ if ( tmp. empty ()
+ && isYear (year)
+ )
+ return Date (year);
+ break;
+ case fmt_YMD:
+ iss >> year >> c1 >> month >> c2 >> day >> tmp;
+ month--;
+ day--;
+ if ( tmp. empty ()
+ && isYear (year)
+ && isMonth (month)
+ && isDay (day)
+ && c1 == c2
+ )
+ return Date (year, (char) month, (char) day);
+ break;
  default: throw runtime_error (FUNC "Unknown date format");
  }
+ return Date ();
 }
 
 
 
-bool Date::operator<= (const Date &other) const
+bool Date::less (const Date &other,
+ bool equal) const
 {
  LESS_PART (*this, other, year);
  LESS_PART (*this, other, month);
  LESS_PART (*this, other, day);
- return true;
+ return equal;
 }
 
 

tsv.hpp

@@ -48,7 +48,7 @@ namespace Common_sp
 
 struct Date : Root
 {
- enum Format {fmt_Year, fmt_None}; // not complete list ??
+ enum Format {fmt_Year, fmt_YMD, fmt_None}; // not complete list ??
  short year {0};
  char month {0};
  // 0 .. 12 - 1
@@ -66,6 +66,10 @@ struct Date : Root
  {}
  static bool isYear (short n)
  { return n > 1000 && n < 2500; } // PAR
+ static bool isMonth (short n)
+ { return between<short> (n, 0, 12); } 
+ static bool isDay (short n)
+ { return between<short> (n, 0, 31); } // Must depend on month ??
  static Date parse (const string &s,
  Format fmt);
  // Return: !empty() <=> success
@@ -94,7 +98,12 @@ struct Date : Root
  && month == other. month
  && day == other. day;
  }
- bool operator<= (const Date &other) const;
+ bool less (const Date &other,
+ bool equal) const;
+ bool operator<= (const Date &other) const
+ { return less (other, true); }
+ bool operator< (const Date &other) const
+ { return less (other, false); }
  Date operator- (const Date &other) const;
  // Requires: other <= *this
 };
@@ -120,6 +129,7 @@ struct TextTable : Named
  static constexpr size_t choices_max {7}; // PAR
  Set<string> choices;
  // size() <= choices_max + 1
+ Header () = default;
  explicit Header (const string &name_arg)
  : Named (name_arg)
  {}

version.txt

@@ -1 +1 @@
-3.12.20
+3.12.21