Ignore whitespace errors, or errors which do not have an error field for FILTER and ID
@@ -97,6 +97,12 @@ namespace ebi
void Fixer::visit(IdBodyError &error)
{
+ if (error.field == "") {
+ util::writeline(output, *line);
+ ignored_errors++;
+ return;
+ }
+
std::cerr << "DEBUG: line " << error.line << ": fixing invalid ID field " << error.field << std::endl;
const size_t id_column_index = 2;
const std::string empty_id_column = ".";
@@ -131,6 +137,12 @@ namespace ebi
void Fixer::visit(FilterBodyError &error)
{
+ if (error.field == "") {
+ util::writeline(output, *line);
+ ignored_errors++;
+ return;
+ }
+
std::cerr << "DEBUG: line " << error.line << ": fixing invalid FILTER field " << error.field << std::endl;
const size_t filter_column_index = 6;
const std::string empty_filter_column = ".";
