+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
+ string filename = outputDir + "get.seqs.debug.report";
+
+ ofstream out;
+ m->openOutputFile(filename, out);
+
+
+ //compare fasta, name, qual and taxonomy if given to make sure they contain the same seqs
+ if (fastafile != "") {
+ if (namefile != "") { //compare with fasta
+ if (sanity["fasta"] != sanity["name"]) { //create mismatch file
+ createMisMatchFile(out, fastafile, namefile, sanity["fasta"], sanity["name"]);
+ }
+ }
+ if (qualfile != "") {
+ if (sanity["fasta"] != sanity["qual"]) { //create mismatch file
+ createMisMatchFile(out, fastafile, qualfile, sanity["fasta"], sanity["qual"]);
+ }
+ }
+ if (taxfile != "") {
+ if (sanity["fasta"] != sanity["tax"]) { //create mismatch file
+ createMisMatchFile(out, fastafile, taxfile, sanity["fasta"], sanity["tax"]);
+ }
+ }
+ }
+
+ //compare dupnames, groups and list if given to make sure they match
+ if (namefile != "") {
+ if (groupfile != "") {
+ if (sanity["dupname"] != sanity["group"]) { //create mismatch file
+ createMisMatchFile(out, namefile, groupfile, sanity["dupname"], sanity["group"]);
+ }
+ }
+ if (listfile != "") {
+ if (sanity["dupname"] != sanity["list"]) { //create mismatch file
+ createMisMatchFile(out, namefile, listfile, sanity["dupname"], sanity["list"]);
+ }
+ }
+ }else{