From: westcott <westcott>
Date: Mon, 23 Aug 2010 16:11:13 +0000 (+0000)
Subject: filter.seqs bug change
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=d84bb41d7dadcfa2c67ce5edb9b94060e5659fa7

filter.seqs bug change
---

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 71436b7..ebe8a90 100644
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -737,8 +737,8 @@
 				A7DA2022113FECD400BF472F /* clustercommand.h */,
 				A71D924311AEB42400D00CBC /* clustersplitcommand.h */,
 				A71D924211AEB42400D00CBC /* clustersplitcommand.cpp */,
-				A7DA2025113FECD400BF472F /* collectcommand.cpp */,
 				A7DA2026113FECD400BF472F /* collectcommand.h */,
+				A7DA2025113FECD400BF472F /* collectcommand.cpp */,
 				A7DA2029113FECD400BF472F /* collectsharedcommand.cpp */,
 				A7DA202A113FECD400BF472F /* collectsharedcommand.h */,
 				A7DA2031113FECD400BF472F /* consensuscommand.cpp */,
diff --git a/aligncommand.cpp b/aligncommand.cpp
index ed6b45d..613f9b7 100644
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -347,7 +347,7 @@ int AlignCommand::execute(){
 				
 #else
 		vector<unsigned long int> positions = divideFile(candidateFileNames[s], processors);
-				
+							
 		for (int i = 0; i < (positions.size()-1); i++) {
 			lines.push_back(new linePair(positions[i], positions[(i+1)]));
 		}	
diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index e91d32b..2c61465 100644
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -866,6 +866,13 @@ int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename)
 				processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 				process++;
 			}else if (pid == 0){
+				//reset child's filter counts to 0;
+				F.a.clear(); F.a.resize(alignmentLength, 0);
+				F.t.clear(); F.t.resize(alignmentLength, 0);
+				F.g.clear(); F.g.resize(alignmentLength, 0);
+				F.c.clear(); F.c.resize(alignmentLength, 0);
+				F.gap.clear(); F.gap.resize(alignmentLength, 0);
+				
 				num = driverCreateFilter(F, filename, lines[process]);
 				
 				//write out filter counts to file
diff --git a/mothur.h b/mothur.h
index 2622e25..d5086b3 100644
--- a/mothur.h
+++ b/mothur.h
@@ -1163,7 +1163,7 @@ inline vector<unsigned long int> divideFile(string filename, int& proc) {
 		//for each process seekg to closest file break and search for next '>' char. make that the filebreak
 		for (int i = 0; i < proc; i++) {
 			unsigned long int spot = (i+1) * chunkSize;
-			
+					
 			ifstream in;
 			openInputFile(filename, in);
 			in.seekg(spot);
@@ -1174,9 +1174,10 @@ inline vector<unsigned long int> divideFile(string filename, int& proc) {
 			   char c = in.get();
 			   if (c == '>') {   in.putback(c); newSpot = in.tellg(); break;  }
 			}
-			
+				
 			//there was not another sequence before the end of the file
-			if (newSpot == spot) {	break;  }
+			unsigned long int sanityPos = in.tellg();
+			if (sanityPos == -1) {	break;  }
 			else {   filePos.push_back(newSpot);  }
 			
 			in.close();