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Github issue 38: unclear error message for scaffold2fasta

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commit 9e382c0e3c57b89f957ed9b5dadfd8932c47518a 1 parent 9e4bc25
@jts authored
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3  src/SGA/scaffold2fasta.cpp
@@ -38,7 +38,8 @@ static const char *SCAFFOLD2FASTA_USAGE_MESSAGE =
" --help display this help and exit\n"
" -v, --verbose display verbose output\n"
" -f, --contig-file=FILE read the contig sequences from FILE\n"
-" -a, --asqg-file=FILE read the sequence graph from FILE. This supercedes --contig-file\n"
+" -a, --asqg-file=FILE read the contig string graph from FILE. This supercedes --contig-file\n"
+" this is usually the output from the sga-assemble step\n"
" --no-singletons do not output scaffolds that consist of a single contig\n"
" -o, --outfile=FILE write the scaffolds to FILE (default: scaffolds.fa)\n"
" -m, --min-length=N only output scaffolds longer than N bases\n"
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8 src/Scaffold/ScaffoldSequenceCollection.cpp
@@ -23,7 +23,13 @@ GraphSequenceCollection::GraphSequenceCollection(StringGraph* pGraph) : m_pGraph
std::string GraphSequenceCollection::getSequence(const std::string& id) const
{
Vertex* pVertex = m_pGraph->getVertex(id);
- assert(pVertex != NULL);
+ if(pVertex == NULL)
+ {
+ std::cerr << "Error: could not find the contig record with id " << id << "\n";
+ std::cerr << "Check to make sure you have loaded the correct set of contigs\n";
+ exit(EXIT_FAILURE);
+ }
+
return pVertex->getSeq().toString();
}
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