From cbaa068e77aeb15bb06f0695a36d8f757977ed64 Mon Sep 17 00:00:00 2001 From: Sarah Westcott Date: Wed, 11 Jul 2012 14:37:24 -0400 Subject: [PATCH] added debug statements to trim.seqs --- trimseqscommand.cpp | 3 +++ 1 file changed, 3 insertions(+) diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp index 6a8afd0..3b9d195 100644 --- a/trimseqscommand.cpp +++ b/trimseqscommand.cpp @@ -607,9 +607,11 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string Sequence currSeq(inFASTA); m->gobble(inFASTA); //cout << currSeq.getName() << '\t' << currSeq.getUnaligned().length() << endl; + if (m->debug) { m->mothurOut("[DEBUG]: " + toString(count) + " fasta = " + currSeq.getName() + '\n'); } QualityScores currQual; if(qFileName != ""){ currQual = QualityScores(qFile); m->gobble(qFile); + if (m->debug) { m->mothurOut("[DEBUG]: qual = " + currQual.getName() + '\n'); } } string origSeq = currSeq.getUnaligned(); @@ -1185,6 +1187,7 @@ int TrimSeqsCommand::setLines(string filename, string qfilename) { } for (int i = 0; i < (fastaFilePos.size()-1); i++) { + if (m->debug) { m->mothurOut("[DEBUG]: " + toString(i) +'\t' + toString(fastaFilePos[i]) + '\t' + toString(fastaFilePos[i+1]) + '\n'); } lines.push_back(linePair(fastaFilePos[i], fastaFilePos[(i+1)])); if (qfilename != "") { qLines.push_back(linePair(qfileFilePos[i], qfileFilePos[(i+1)])); } } -- 2.39.2