X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimflowscommand.cpp;h=5800cde2146f108ae6efc3d1bce50b9bb9913750;hb=aca78ed4a47dff8672ea8fd93cef0dfbaf0f7495;hp=2da240e21b5103d4d77b6eb24d0f0c335f3a7d3c;hpb=b0997605981902442138b9309e9c43d95c3ba10a;p=mothur.git

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index 2da240e..5800cde 100644
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -47,6 +47,7 @@ string TrimFlowsCommand::getHelpString(){
 	try {
 		string helpString = "";
 		helpString += "The trim.flows command reads a flowgram file and creates .....\n";
+        helpString += "The order parameter options are A, B or I.  Default=A. A = TACG and B = TACGTACGTACGATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGC and I = TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGC.\n";
 		helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
 		helpString += "For more details please check out the wiki http://www.mothur.org/wiki/Trim.flows.\n";
 		return helpString;
@@ -394,7 +395,7 @@ int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileN
 		
 		if(line->start == 0){
 			flowFile >> numFlows; m->gobble(flowFile);
-			scrapFlowFile << maxFlows << endl;
+			scrapFlowFile << numFlows << endl;
 			trimFlowFile << maxFlows << endl;
 			if(allFiles){
 				for(int i=0;i<thisBarcodePrimerComboFileNames.size();i++){
@@ -434,7 +435,11 @@ int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileN
 				success = 0;
 				trashCode += 'l';
 			}
-			
+            if(!flowData.hasGoodHomoP()){	//screen to see if sequence meets the maximum homopolymer limit
+				success = 0;
+				trashCode += 'h';
+			}
+
 			int primerIndex = 0;
 			int barcodeIndex = 0;
 			
@@ -594,6 +599,7 @@ void TrimFlowsCommand::getOligos(vector<vector<string> >& outFlowFileNames){
 				else if(type == "REVERSE"){
 					string oligoRC = reverseOligo(oligo);
 					revPrimer.push_back(oligoRC);
+                    if (m->debug) { m->mothurOut("[DEBUG]: reverse oligos = " + oligoRC + ".\n"); }
 				}
 				else if(type == "BARCODE"){
 					oligosFile >> group;
@@ -632,8 +638,7 @@ void TrimFlowsCommand::getOligos(vector<vector<string> >& outFlowFileNames){
 			primers[""] = 0;
 			primerNameVector.push_back("");			
 		}
-		
-		
+
 		outFlowFileNames.resize(barcodeNameVector.size());
 		for(int i=0;i<outFlowFileNames.size();i++){
 			outFlowFileNames[i].assign(primerNameVector.size(), "");
@@ -820,7 +825,7 @@ int TrimFlowsCommand::createProcessesCreateTrim(string flowFileName, string trim
 		
 		//loop through and create all the processes you want
 		while (process != processors) {
-			int pid = fork();
+			pid_t pid = fork();
 			
 			if (pid > 0) {
 				processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
@@ -832,7 +837,7 @@ int TrimFlowsCommand::createProcessesCreateTrim(string flowFileName, string trim
 					for(int i=0;i<tempBarcodePrimerComboFileNames.size();i++){
 						for(int j=0;j<tempBarcodePrimerComboFileNames[0].size();j++){
                             if (tempBarcodePrimerComboFileNames[i][j] != "") {
-                                tempBarcodePrimerComboFileNames[i][j] += toString(getpid()) + ".temp";
+                                tempBarcodePrimerComboFileNames[i][j] += m->mothurGetpid(process) + ".temp";
                                 ofstream temp;
                                 m->openOutputFile(tempBarcodePrimerComboFileNames[i][j], temp);
                                 temp.close();
@@ -841,9 +846,9 @@ int TrimFlowsCommand::createProcessesCreateTrim(string flowFileName, string trim
 					}
 				}
 				driverCreateTrim(flowFileName,
-								 (trimFlowFileName + toString(getpid()) + ".temp"),
-								 (scrapFlowFileName + toString(getpid()) + ".temp"),
-								 (fastaFileName + toString(getpid()) + ".temp"),
+								 (trimFlowFileName + m->mothurGetpid(process) + ".temp"),
+								 (scrapFlowFileName + m->mothurGetpid(process) + ".temp"),
+								 (fastaFileName + m->mothurGetpid(process) + ".temp"),
 								 tempBarcodePrimerComboFileNames, lines[process]);
 
 				exit(0);