From 51ccd55dad9ce1bb21e8ea6eedc54a8b66a3962e Mon Sep 17 00:00:00 2001
From: Cong <congm1@andrew.cmu.edu>
Date: Sun, 22 Apr 2018 09:04:08 -0400
Subject: [PATCH] update stdout log

---
 src/main.cpp | 49 +++++++------------------------------------------
 1 file changed, 7 insertions(+), 42 deletions(-)

diff --git a/src/main.cpp b/src/main.cpp
index 2e982b6..2cd61f2 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -15,6 +15,9 @@ See LICENSE for licensing.
 using namespace std;
 
 int main(int argc, char* argv[]){
+	time_t CurrentTime;
+	string CurrentTimeStr;
+	
 	bool success=parse_arguments(argc, argv);
 
 	if(success){
@@ -65,47 +68,9 @@ int main(int argc, char* argv[]){
 				OutputNewGenome(SegmentGraph, Components, RefSequence, RefName, Output_Prefix+"_genome.fa");
 		}
 
-		/*sort(SegmentGraph.vEdges.begin(), SegmentGraph.vEdges.end(),  [](Edge_t a, Edge_t b){return a.Weight>b.Weight;});
-		ofstream output3(Output_Prefix+"_discordantedges.txt", ios::out);
-		output3<<"# ";
-		for(int i=0; i<argc; i++)
-			output3<<argv[i]<<" ";
-		output3<<endl;
-		output3<<"# Ind1\tNode1\tHead1\tInd2\tNode2\tHead2\tWeight\n";
-		for(int i=0; i<SegmentGraph.vEdges.size(); i++){
-			int ind1=SegmentGraph.vEdges[i].Ind1, ind2=SegmentGraph.vEdges[i].Ind2;
-			if(SegmentGraph.vNodes[ind1].Chr!=SegmentGraph.vNodes[ind2].Chr || (SegmentGraph.vNodes[ind2].Position-SegmentGraph.vNodes[ind1].Position-SegmentGraph.vNodes[ind1].Length>Concord_Dist_Pos && ind2-ind1>20) || SegmentGraph.vEdges[i].Head1!=false || SegmentGraph.vEdges[i].Head2!=true){
-				bool flag=false;
-				pair<int,int> pos1=Node_NewChr[SegmentGraph.vEdges[i].Ind1], pos2=Node_NewChr[SegmentGraph.vEdges[i].Ind2];
-				if(pos1.first==pos2.first && pos1.second<pos2.second && SegmentGraph.vEdges[i].Head1==(Components[pos1.first][pos1.second]<0) && SegmentGraph.vEdges[i].Head2==(Components[pos2.first][pos2.second]>0))
-					flag=true;
-				else if(pos1.first==pos2.first && pos1.second>pos2.second && SegmentGraph.vEdges[i].Head2==(Components[pos2.first][pos2.second]<0) && SegmentGraph.vEdges[i].Head1==(Components[pos1.first][pos1.second]>0))
-					flag=true;
-				if(flag){
-					map<Edge_t, vector< pair<int,int> > >::iterator itmap=ExactBP.find(SegmentGraph.vEdges[i]);
-					vector< pair<int,int> > BP;
-					if(itmap==ExactBP.end() || itmap->second.size()==0){
-						int bp1,bp2;
-						bp1=(SegmentGraph.vEdges[i].Head1?SegmentGraph.vNodes[SegmentGraph.vEdges[i].Ind1].Position:(SegmentGraph.vNodes[SegmentGraph.vEdges[i].Ind1].Position+SegmentGraph.vNodes[SegmentGraph.vEdges[i].Ind1].Length));
-						bp2=(SegmentGraph.vEdges[i].Head2?SegmentGraph.vNodes[SegmentGraph.vEdges[i].Ind2].Position:(SegmentGraph.vNodes[SegmentGraph.vEdges[i].Ind2].Position+SegmentGraph.vNodes[SegmentGraph.vEdges[i].Ind2].Length));
-						BP.push_back(make_pair(bp1,bp2));
-					}
-					else
-						BP=itmap->second;
-					for(int k=0; k<BP.size(); k++){
-						if(SegmentGraph.vEdges[i].Head1)
-							output3<<SegmentGraph.vEdges[i].Ind1<<'\t'<<SegmentGraph.vNodes[SegmentGraph.vEdges[i].Ind1].Chr<<','<<BP[k].first<<","<<(SegmentGraph.vNodes[SegmentGraph.vEdges[i].Ind1].Position+SegmentGraph.vNodes[SegmentGraph.vEdges[i].Ind1].Length-BP[k].first)<<"\tH\t";
-						else
-							output3<<SegmentGraph.vEdges[i].Ind1<<'\t'<<SegmentGraph.vNodes[SegmentGraph.vEdges[i].Ind1].Chr<<','<<SegmentGraph.vNodes[SegmentGraph.vEdges[i].Ind1].Position<<","<<(BP[k].first-SegmentGraph.vNodes[SegmentGraph.vEdges[i].Ind1].Position)<<"\tT\t";
-						if(SegmentGraph.vEdges[i].Head2)
-							output3<<SegmentGraph.vEdges[i].Ind2<<'\t'<<SegmentGraph.vNodes[SegmentGraph.vEdges[i].Ind2].Chr<<','<<BP[k].second<<","<<(SegmentGraph.vNodes[SegmentGraph.vEdges[i].Ind2].Position+SegmentGraph.vNodes[SegmentGraph.vEdges[i].Ind2].Length-BP[k].second)<<"\tH\t";
-						else
-							output3<<SegmentGraph.vEdges[i].Ind2<<'\t'<<SegmentGraph.vNodes[SegmentGraph.vEdges[i].Ind2].Chr<<','<<SegmentGraph.vNodes[SegmentGraph.vEdges[i].Ind2].Position<<","<<(BP[k].second-SegmentGraph.vNodes[SegmentGraph.vEdges[i].Ind2].Position)<<"\tT\t";
-						output3<<SegmentGraph.vEdges[i].Weight<<endl;
-					}
-				}
-			}
-		}
-		output3.close();*/
+		time(&CurrentTime);
+		CurrentTimeStr=ctime(&CurrentTime);
+		cout<<"["<<CurrentTimeStr.substr(0, CurrentTimeStr.size()-1)<<"] Done."<<endl;
+
 	}
 }