Fixed bug with parsing name field in bedFile.cpp

c3989a1a · Aaron · 64df6024 · c3989a1a · c3989a1a · c3989a1a
Commit c3989a1a authored 15 years ago by Aaron
--- a/bin/closestBed
+++ b/bin/closestBed
--- a/bin/complementBed
+++ b/bin/complementBed
--- a/bin/coverageBed
+++ b/bin/coverageBed
--- a/bin/fastaFromBed
+++ b/bin/fastaFromBed
--- a/bin/genomeCoverageBed
+++ b/bin/genomeCoverageBed
--- a/bin/intersectBed
+++ b/bin/intersectBed
--- a/bin/linksBed
+++ b/bin/linksBed
--- a/bin/mergeBed
+++ b/bin/mergeBed
--- a/bin/peIntersectBed
+++ b/bin/peIntersectBed
--- a/bin/sortBed
+++ b/bin/sortBed
--- a/bin/subtractBed
+++ b/bin/subtractBed
--- a/bin/windowBed
+++ b/bin/windowBed
--- a/obj/bedFile.o
+++ b/obj/bedFile.o
--- a/src/utils/bedFile/bedFile.cpp
+++ b/src/utils/bedFile/bedFile.cpp
@@ -211,7 +211,7 @@ bool BedFile::parseBedLine (BED &bed, const vector<string> &lineVector, const in
 			bed.end = atoi(lineVector[2].c_str());
 			bed.name = "";
 			bed.score = "";
-			bed.strand = "+";
+			bed.strand = "";
 			return true;
 		}
 		else if (this->bedType == 4) {
@@ -220,7 +220,7 @@ bool BedFile::parseBedLine (BED &bed, const vector<string> &lineVector, const in
 			bed.end = atoi(lineVector[2].c_str());
 			bed.name = lineVector[3];
 			bed.score = "";
-			bed.strand = "+";
+			bed.strand = "";
 			return true;
 		}
 		else if (this->bedType ==5) {
@@ -229,7 +229,7 @@ bool BedFile::parseBedLine (BED &bed, const vector<string> &lineVector, const in
 			bed.end = atoi(lineVector[2].c_str());
 			bed.name = lineVector[3];
 			bed.score = lineVector[4];
-			bed.strand = "+";
+			bed.strand = "";
 			return true;			
 		}
 		else if (this->bedType == 6) {
@@ -262,6 +262,9 @@ bool BedFile::parseBedLine (BED &bed, const vector<string> &lineVector, const in
 			bed.chrom = lineVector[0];
 			bed.start = atoi(lineVector[1].c_str());
 			bed.end = atoi(lineVector[2].c_str());
+			bed.name = "";
+			bed.score = "";
+			bed.strand = "";
 			return true;
 		}
 		else if (this->bedType == 4) {
@@ -269,6 +272,8 @@ bool BedFile::parseBedLine (BED &bed, const vector<string> &lineVector, const in
 			bed.start = atoi(lineVector[1].c_str());
 			bed.end = atoi(lineVector[2].c_str());
 			bed.name = lineVector[3];
+			bed.score = "";
+			bed.strand = "+";
 			return true;
 		}
 		else if (this->bedType ==5) {
@@ -276,7 +281,8 @@ bool BedFile::parseBedLine (BED &bed, const vector<string> &lineVector, const in
 			bed.start = atoi(lineVector[1].c_str());
 			bed.end = atoi(lineVector[2].c_str());
 			bed.name = lineVector[3];
-			bed.score = atoi(lineVector[4].c_str());
+			bed.score = lineVector[4];
+			bed.strand = "";
 			return true;			
 		}
 		else if (this->bedType == 6) {
@@ -284,7 +290,7 @@ bool BedFile::parseBedLine (BED &bed, const vector<string> &lineVector, const in
 			bed.start = atoi(lineVector[1].c_str());
 			bed.end = atoi(lineVector[2].c_str());
 			bed.name = lineVector[3];
-			bed.score = atoi(lineVector[4].c_str());
+			bed.score = lineVector[4];
 			bed.strand = lineVector[5];
 			return true;
 		}