added sequence name to error string in fastq.info. Changed np_shannon to npshannon.

diff --git a/collectcommand.cpp b/collectcommand.cpp
index e0d62dd5ddd7acd106d18af31de013f6fce9c462..7ad41367f795abe7aeeda1052a8211daf72aeaf4 100644 (file)
--- a/collectcommand.cpp
+++ b/collectcommand.cpp
@@ -44,7 +44,7 @@ vector<string> CollectCommand::setParameters(){
                CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);
                CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
                CommandParameter pfreq("freq", "Number", "", "100", "", "", "",false,false); parameters.push_back(pfreq);
-               CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-np_shannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap-geometric-qstat-logseries-bergerparker-bstick-goodscoverage-efron-boneh-solow-shen", "sobs-chao-ace-jack-shannon-npshannon-simpson", "", "", "",true,false); parameters.push_back(pcalc);
+               CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-npshannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap-geometric-qstat-logseries-bergerparker-bstick-goodscoverage-efron-boneh-solow-shen", "sobs-chao-ace-jack-shannon-npshannon-simpson", "", "", "",true,false); parameters.push_back(pcalc);
                CommandParameter pabund("abund", "Number", "", "10", "", "", "",false,false); parameters.push_back(pabund);
                CommandParameter psize("size", "Number", "", "0", "", "", "",false,false); parameters.push_back(psize);
                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
@@ -94,7 +94,7 @@ CollectCommand::CollectCommand(){
                outputTypes["jack"] = tempOutNames;
                outputTypes["shannon"] = tempOutNames;
                outputTypes["shannoneven"] = tempOutNames;
-               outputTypes["np_shannon"] = tempOutNames;
+               outputTypes["npshannon"] = tempOutNames;
                outputTypes["heip"] = tempOutNames;
                outputTypes["smithwilson"] = tempOutNames;
                outputTypes["simpson"] = tempOutNames;
@@ -151,7 +151,7 @@ CollectCommand::CollectCommand(string option)  {
                        outputTypes["jack"] = tempOutNames;
                        outputTypes["shannon"] = tempOutNames;
                        outputTypes["shannoneven"] = tempOutNames;
-                       outputTypes["np_shannon"] = tempOutNames;
+                       outputTypes["npshannon"] = tempOutNames;
                        outputTypes["heip"] = tempOutNames;
                        outputTypes["smithwilson"] = tempOutNames;
                        outputTypes["simpson"] = tempOutNames;
@@ -346,8 +346,8 @@ int CollectCommand::execute(){
                                                cDisplays.push_back(new CollectDisplay(new ShannonEven(), new OneColumnFile(fileNameRoot+"shannoneven")));
                                                outputNames.push_back(fileNameRoot+"shannoneven"); outputTypes["shannoneven"].push_back(fileNameRoot+"shannoneven");
                                        }else if (Estimators[i] == "npshannon") { 
-                                               cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(fileNameRoot+"np_shannon")));
-                                               outputNames.push_back(fileNameRoot+"np_shannon"); outputTypes["np_shannon"].push_back(fileNameRoot+"np_shannon");
+                                               cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(fileNameRoot+"npshannon")));
+                                               outputNames.push_back(fileNameRoot+"npshannon"); outputTypes["npshannon"].push_back(fileNameRoot+"npshannon");
                                        }else if (Estimators[i] == "heip") { 
                                                cDisplays.push_back(new CollectDisplay(new Heip(), new OneColumnFile(fileNameRoot+"heip")));
                                                outputNames.push_back(fileNameRoot+"heip"); outputTypes["heip"].push_back(fileNameRoot+"heip");

diff --git a/parsefastaqcommand.cpp b/parsefastaqcommand.cpp
index 9509a20af2528392c2df8590aea61fef6a7665b4..730873a4bd64e5409c5e3580bfd15338179a787c 100644 (file)
--- a/parsefastaqcommand.cpp
+++ b/parsefastaqcommand.cpp
@@ -166,7 +166,7 @@ int ParseFastaQCommand::execute(){
                        
                        //sanity check sequence length and number of quality scores match
                        if (name2 != "") { if (name != name2) { m->mothurOut("[ERROR]: names do not match. read " + name + " for fasta and " + name2 + " for quality."); m->mothurOutEndLine(); m->control_pressed = true; break; } }
-                       if (quality.length() != sequence.length()) { m->mothurOut("[ERROR]: lengths do not match. read " + toString(sequence.length()) + " characters for fasta and " + toString(quality.length()) + " characters for quality scores."); m->mothurOutEndLine(); m->control_pressed = true; break; }
+                       if (quality.length() != sequence.length()) { m->mothurOut("[ERROR]: Lengths do not match for sequence " + name + ". Read " + toString(sequence.length()) + " characters for fasta and " + toString(quality.length()) + " characters for quality scores."); m->mothurOutEndLine(); m->control_pressed = true; break; }
                        
                        //print sequence info to files
                        if (fasta) { outFasta << ">" << name << endl << sequence << endl; }

diff --git a/summarycommand.cpp b/summarycommand.cpp
index 022b174a5c21f4de6f26c2dcd8232b0744da8120..83ea8c9b4b5ab077283454089b35d9de13908003 100644 (file)
--- a/summarycommand.cpp
+++ b/summarycommand.cpp
@@ -42,7 +42,7 @@ vector<string> SummaryCommand::setParameters(){
                CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(psabund);
                CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);
                CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
-               CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-np_shannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap-geometric-qstat-logseries-bergerparker-bstick-goodscoverage-efron-boneh-solow-shen", "sobs-chao-ace-jack-shannon-npshannon-simpson", "", "", "",true,false); parameters.push_back(pcalc);
+               CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-npshannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap-geometric-qstat-logseries-bergerparker-bstick-goodscoverage-efron-boneh-solow-shen", "sobs-chao-ace-jack-shannon-npshannon-simpson", "", "", "",true,false); parameters.push_back(pcalc);
                CommandParameter pabund("abund", "Number", "", "10", "", "", "",false,false); parameters.push_back(pabund);
                CommandParameter psize("size", "Number", "", "0", "", "", "",false,false); parameters.push_back(psize);
                CommandParameter pgroupmode("groupmode", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pgroupmode);