PD-4755 calling fusion2geneSymbols() for a mutation protein

amr_report.cpp

@@ -808,7 +808,7 @@ struct BlastAlignment : Alignment
     }
 public:
   string fusion2geneSymbols () const
-    { ASSERT (! isMutationProt ());   
+    { ASSERT (! isMutationProt ());
       if (fusions. empty ())
         return getGeneSymbol ();
       string s;
@@ -1102,6 +1102,7 @@ struct BlastAlignment : Alignment
         	 )
           if (   ! targetProt 
               || (   ! isMutationProt ()   // PD-4722
+                  && ! other. isMutationProt ()   // PD-4755
                   && fusion2geneSymbols () != other. fusion2geneSymbols ()
                  )
              )  // PD-4687
@@ -1397,7 +1398,7 @@ struct Batch
   	  	  }
   	  	  catch (const exception &e)
   	  	  {
-  	  	    throw runtime_error ("Cannot read " + famFName +", line " + toString (f. lineNum) + "\n" + e. what ());
+  	  	    throw runtime_error ("Cannot read " + famFName +", " + f. lineStr () + "\n" + e. what ());
   	  	  }
 	  	}
 	    {

amrfinder.cpp

@@ -33,8 +33,9 @@
 *               gunzip (optional)
 *
 * Release changes:
+*   3.11.21 10/02/2023 PD-4755  bug: calling fusion2geneSymbols() for a mutation protein
 *   3.11.20 09/06/2023 PD-4722  bug: calling fusion2geneSymbols() for a mutation protein
-*                               TERM codes are printed only when output is to screen
+*                               color codes are printed only when output is to screen
 *   3.11.19 08/09/2023 PD-4698  if a pseudogene is overlapped by a different gene on the length >= 20 aa with the same gene symbol then the pseudogene is not reported
 *           08/04/2023 PD-4706  protein match overrides a nucleotide match for point mutations
 *   3.11.18 07/25/2023          parameter order in instruction; "can be gzipped" is added to help

common.cpp

@@ -1150,7 +1150,7 @@ void copyText (const string &inFName,
   QC_ASSERT (os. good ());
   LineInput li (inFName);
   while (li. nextLine ())
-    if (li. lineNum > skipLines)
+    if ((size_t) li. lineNum > skipLines)
       os << li. line << endl;
 }
 
@@ -2044,6 +2044,31 @@ void Progress::report () const
 
 
 
+// TextPos
+
+void TextPos::inc (bool eol_arg)
+{ 
+ 	if (eol ())
+ 		lineNum++;
+  if (eol_arg)
+  	charNum = eol_pos;
+  else
+  	charNum++;
+  ASSERT (eol_arg == eol ());
+}
+
+
+
+void TextPos::dec ()
+{ 
+	if (! charNum)
+		lineNum--;
+	charNum--;  
+}
+
+
+
+
 // Input
 
 Input::Input (const string &fName,
@@ -2099,7 +2124,11 @@ bool LineInput::nextLine ()
   try 
 	{
     getline (*is, line);  // faster than readLine(*is,line)
-  	eof = is->eof ();
+
+		eof = is->eof ();
+		if (! eof)
+			lineNum++;
+
   	const bool end = line. empty () && eof;
 
     if (! commentStart. empty ())
@@ -2110,8 +2139,6 @@ bool LineInput::nextLine ()
     }
   //trimTrailing (line); 
 
-  	lineNum++;
-
   	if (! end)
   		prog ();
 
@@ -2126,91 +2153,38 @@ bool LineInput::nextLine ()
 
 
 
-// ObjectInput
-
-bool ObjectInput::next (Root &row)
-{ 
-  QC_ASSERT (is);
-
-	row. clear ();
-
-	if (eof)
-	  return false;
-
-	row. read (*is);
-	row. qc ();
-	lineNum++;
-
- 	eof = is->eof ();
-  if (eof)
-  {
-  	ASSERT (row. empty ());
-  	return false;
-  }
-
-	prog ();
-
-  ASSERT (is->peek () == '\n');
-
-  skipLine (*is);
-
-	return true;
-}
-
-
-
 // CharInput
 
 char CharInput::get ()
 { 
-  ASSERT (is);
-  QC_ASSERT (! eof);
-
-  ungot = false;
+  ASSERT (is);  
 
-  const char c = (char) is->get ();
+  const char c = (char) is->get ();    
 
 	eof = is->eof ();	
   QC_ASSERT (eof == (c == (char) EOF));
+	if (! eof)
+	  tp. inc (c == '\n');  // UNIX
+	ungot = false;	  
 
-  if (eol)  // previous char
-  { 
-    lineNum++;
-    charNum = 0;
-  }
-  else
-    charNum++;
-
-  eol_prev = eol;
-	eol = (eof || c == '\n');  // UNIX
-  if (eol)
+  if (tp. eol ())
     prog ();
 
-#if 0
-	PRINT (c);
-	PRINT (lineNum);
-	PRINT (charNum);
-#endif
-
 	return c;
 }
 
 
 
 void CharInput::unget ()
 { 
-  ASSERT (is);
 	QC_ASSERT (! ungot);
-  QC_ASSERT (! eof);
-
-	ungot = true;
-
-  is->unget (); 
-	charNum--;  // May be (uint) (-1)
-	eof = false;
-  eol = eol_prev;
-  if (eol)
-    lineNum--;
+  QC_ASSERT (! eof);  
+
+  ASSERT (is);
+  is->unget ();   
+  tp. dec ();
+
+  ungot = true;
 }
 
 
@@ -2221,7 +2195,7 @@ string CharInput::getLine ()
   while (! eof)
   {
     const char c = get ();
-    if (eol)
+    if (tp. eol ())
       break;
     s += c;
   }
@@ -2247,7 +2221,7 @@ void Token::readInput (CharInput &in,
 	if (in. eof)
 		return;  
 
-	charNum = in. charNum;
+	tp = in. tp;
 
 	if (   c == '\'' 
 	    || c == '\"'
@@ -2261,7 +2235,7 @@ void Token::readInput (CharInput &in,
 			c = in. get (); 
 			if (in. eof && (! consecutiveQuotesInText || ! prevQuote))
 		    in. error ("Text is not finished: end of file", false);
-			if (in. eol)
+			if (in. tp. eol ())
 		    continue;
 			if (c == quote)
 			{
@@ -2340,7 +2314,7 @@ void Token::readInput (CharInput &in,
   qc ();
 
   if (verbose ())
-  	cout << type2str (type) << ' ' << *this << ' ' << charNum + 1 << endl;
+  	cout << type2str (type) << ' ' << *this << ' ' << tp. str () << endl;
 }
 
 
@@ -2518,7 +2492,7 @@ Token TokenInput::getXmlText ()
 
 
   Token t;
-  t. charNum = ci. charNum;
+  t. tp = ci. tp;
   size_t htmlTags = 0;
   bool prevSlash = false;
 	for (;;)
@@ -2633,7 +2607,7 @@ Token TokenInput::getXmlComment ()
   QC_ASSERT (ci. get () == '-');
 
   Token t;
-  t. charNum = ci. charNum;
+  t. tp = ci. tp;
   array<char,4> lastChars {{'-', '-', '\0', '\0'}};
   size_t i = 2; 
 	for (;;)
@@ -2676,7 +2650,7 @@ Token TokenInput::getXmlProcessingInstruction ()
   // Embedded processing instructions ??
 
   Token t;
-  t. charNum = ci. charNum;
+  t. tp = ci. tp;
 	for (;;)
 	{ 
 	  char c = ci. get (); 
@@ -2707,7 +2681,7 @@ Token TokenInput::getXmlMarkupDeclaration ()
   QC_ASSERT (last. empty ());
 
   Token t;
-  t. charNum = ci. charNum;
+  t. tp = ci. tp;
 	for (;;)
 	{ 
 	  char c = ci. get ();