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#include <string>
#include <iostream>
#include "error_checker.h"
using namespace std;
void error_checker::add_bad_name(string contig, string entry)
{
num_unrecognized_iworm_contig_names++;
if (num_unrecognized_iworm_contig_names <= 10) {
cerr << "warning, inchworm contig (" << contig << ") isn't recognized. Ignoring entry: [[" << entry << "]]";
}
if (num_unrecognized_iworm_contig_names == 11) {
cerr << "warning, too many unrecognized inchworm contig names. Will report summary of counts later.";
}
}
void error_checker::add_single_read(string read)
{
// must have mixed in a single read with the pairs...
if (num_warnings <= 10) {
cerr << "warning, ignoring read: " << read << "since cannot decipher if /1 or /2 of a pair.";
}
else if (num_warnings == 11) {
cerr << "number of read warnings exceeded 10. Turning off warning messages from here out.\n";
}
num_warnings++;
}
void error_checker::report() const
{
if (num_warnings) {
cerr << "WARNING: note there were " << num_warnings << " reads that could not be deciphered as being /1 or /2 of a PE fragment. Hopefully, these were SE reads that should have been ignored. Otherwise, please research this further.\n\n";
}
if (num_unrecognized_iworm_contig_names) {
cerr << "WARNING: note, there were " << num_unrecognized_iworm_contig_names << " inchworm contig names in the SAM file that were ignored due to the inchworm contig accession not being recognized.\n";
}
}
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