X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sffinfocommand.cpp;h=3562dcc3e88265a93c23af38fa69b3b2c776e4c1;hb=bf83aa09a52403a2faf1a1f82489d1e0c8c32283;hp=66409e88f9013abd8deb9fd2ba78f6bfdf249a38;hpb=3e2465c16d187247ce3befd29811c2d5dfc15ee8;p=mothur.git

diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp
index 66409e8..3562dcc 100644
--- a/sffinfocommand.cpp
+++ b/sffinfocommand.cpp
@@ -316,7 +316,7 @@ int SffInfoCommand::extractSffInfo(string input, string accnos){
 		if (sfftxt) { m->openOutputFile(sfftxtFileName, outSfftxt); outSfftxt.setf(ios::fixed, ios::floatfield); outSfftxt.setf(ios::showpoint);  outputNames.push_back(sfftxtFileName);  outputTypes["sfftxt"].push_back(sfftxtFileName); }
 		if (fasta)	{ m->openOutputFile(outFastaFileName, outFasta);	outputNames.push_back(outFastaFileName); outputTypes["fasta"].push_back(outFastaFileName); }
 		if (qual)	{ m->openOutputFile(outQualFileName, outQual);		outputNames.push_back(outQualFileName); outputTypes["qual"].push_back(outQualFileName);  }
-		if (flow)	{ m->openOutputFile(outFlowFileName, outFlow);		outputNames.push_back(outFlowFileName);  outputTypes["flow"].push_back(outFlowFileName);  }
+		if (flow)	{ m->openOutputFile(outFlowFileName, outFlow);		outputNames.push_back(outFlowFileName);  outFlow.setf(ios::fixed, ios::floatfield); outFlow.setf(ios::showpoint); outputTypes["flow"].push_back(outFlowFileName);  }
 		
 		ifstream in;
 		in.open(input.c_str(), ios::binary);
@@ -331,8 +331,9 @@ int SffInfoCommand::extractSffInfo(string input, string accnos){
 		if (header.version != "0001") { m->mothurOut("Version is not supported, only support version 0001."); m->mothurOutEndLine(); return count; }
 	
 		//print common header
-		if (sfftxt) { printCommonHeader(outSfftxt, header); }
-	
+		if (sfftxt) {	printCommonHeader(outSfftxt, header);		}
+		if (flow)	{	outFlow << header.numFlowsPerRead << endl;	}
+			
 		//read through the sff file
 		while (!in.eof()) {
 			
@@ -778,10 +779,16 @@ int SffInfoCommand::printQualSeqData(ofstream& out, seqRead& read, Header& heade
 //**********************************************************************************************************************
 int SffInfoCommand::printFlowSeqData(ofstream& out, seqRead& read, Header& header) {
 	try {
+		if(header.clipQualRight > header.clipQualLeft){
+			
+			int rightIndex = 0;
+			for (int i = 0; i < header.clipQualRight; i++) {  rightIndex +=  read.flowIndex[i];	}
+
+			out << header.name << ' ' << rightIndex;
+			for (int i = 0; i < read.flowgram.size(); i++) { out << setprecision(2) << ' ' << (read.flowgram[i]/(float)100);  }
+			out << endl;
+		}
 		
-		out << ">" << header.name << " xy=" << header.xy << endl;
-		for (int i = 0; i < read.flowgram.size(); i++) { out << setprecision(2) << (read.flowgram[i]/(float)100) << '\t';  }
-		out << endl;
 		
 		return 0;
 	}