outputNames.push_back(trimSeqFile); outputTypes["fasta"].push_back(trimSeqFile);
string badSeqFile = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pcr.scrap.fasta";
- outputNames.push_back(badSeqFile); outputTypes["fasta"].push_back(badSeqFile);
+
length = 0;
if(oligosfile != ""){ readOligos(); } if (m->control_pressed) { return 0; }
//don't write or keep if blank
if (badNames.size() != 0) { writeAccnos(badNames); }
if (m->isBlank(badSeqFile)) { m->mothurRemove(badSeqFile); }
+ else { outputNames.push_back(badSeqFile); outputTypes["fasta"].push_back(badSeqFile); }
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
if (namefile != "") { readName(badNames); }
}
}
}
-
+
+ //trimming removed all bases
+ if (currSeq.getUnaligned() == "") { goodSeq = false; }
+
if(goodSeq == 1) { currSeq.printSequence(goodFile); }
else {
badSeqNames.insert(currSeq.getName());