Added assert ScaffoldRecord::introduceGap to catch case where the exp…

…ected overlap between scaffold components is not sane.
jts · Oct 11, 2010 · a970410 · a970410
1 parent 140c6dc
commit a970410
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diff --git a/src/SGA/scaffold2fasta.cpp b/src/SGA/scaffold2fasta.cpp
@@ -100,7 +100,7 @@ int scaffold2fastaMain(int argc, char** argv)
     std::cout << "Find overlaps: " << (opt::resolveMask & RESOLVE_OVERLAP) << "\n";
 
     if(opt::asqgFile.empty())
-        assert(false && "only asqg file is implemented atm");
+        assert(false && "only asqg mode is implemented, please provide an ASQG file");
 
     StringGraph* pGraph = SGUtil::loadASQG(opt::asqgFile, 0, true);
     std::istream* pReader = new std::ifstream(opt::scafFile.c_str());

diff --git a/src/Scaffold/ScaffoldRecord.cpp b/src/Scaffold/ScaffoldRecord.cpp
@@ -288,6 +288,7 @@ bool ScaffoldRecord::introduceGap(const std::string& contigString, const Scaffol
         // Truncate the string using the expected overlap and add a gap with a fixed number of Ns
         out.append(10, 'N');
         int expectedOverlap = -1 * link.distance;
+        assert(expectedOverlap < (int)contigString.length());
         out.append(contigString.substr(expectedOverlap));
     }
     else