diff --git a/src/utils/bedFile/bedFile.cpp b/src/utils/bedFile/bedFile.cpp
index 448e25d1510ed3f5c70a850a45178a07ee9c1d5a..dda672ecbbb52ae2fd57266746607d8594b1b6e8 100755
--- a/src/utils/bedFile/bedFile.cpp
+++ b/src/utils/bedFile/bedFile.cpp
@@ -10,7 +10,7 @@
// Acknowledgments: Much of the code herein is taken from Jim Kent's
// BED processing code. I am grateful for his elegant
// genome binning algorithm and therefore use it extensively.
-
+
#include "bedFile.h"
@@ -26,20 +26,20 @@ static int binOffsets[] = {512+64+8+1, 64+8+1, 8+1, 1, 0};
void Tokenize(const string& str, vector<string>& tokens)
{
- // Skip delimiters at beginning.
- string::size_type lastPos = str.find_first_not_of("\t", 0);
- // Find first "non-delimiter".
- string::size_type pos = str.find_first_of("\t", lastPos);
-
- while (string::npos != pos || string::npos != lastPos)
- {
- // Found a token, add it to the vector.
- tokens.push_back(str.substr(lastPos, pos - lastPos));
- // Skip delimiters. Note the "not_of"
- lastPos = str.find_first_not_of("\t", pos);
- // Find next "non-delimiter"
- pos = str.find_first_of("\t", lastPos);
- }
+ // Skip delimiters at beginning.
+ string::size_type lastPos = str.find_first_not_of("\t", 0);
+ // Find first "non-delimiter".
+ string::size_type pos = str.find_first_of("\t", lastPos);
+
+ while (string::npos != pos || string::npos != lastPos)
+ {
+ // Found a token, add it to the vector.
+ tokens.push_back(str.substr(lastPos, pos - lastPos));
+ // Skip delimiters. Note the "not_of"
+ lastPos = str.find_first_not_of("\t", pos);
+ // Find next "non-delimiter"
+ pos = str.find_first_of("\t", lastPos);
+ }
}
int overlaps(const int aS, const int aE, const int bS, const int bE) {
@@ -96,7 +96,10 @@ bool byChromThenStart(BED const & a, BED const & b){
//************************************************
static int getBin(int start, int end)
-/* Given start,end in chromosome coordinates assign it
+/*
+ NOTE: Taken ~verbatim from kent source.
+
+ Given start,end in chromosome coordinates assign it
* a bin. There's a bin for each 128k segment, for each
* 1M segment, for each 8M segment, for each 64M segment,
* and for each chromosome (which is assumed to be less than
@@ -120,8 +123,12 @@ static int getBin(int start, int end)
void BedFile::binKeeperFind(map<int, vector<BED>, std::less<int> > &bk, const int start, const int end, vector<BED> &hits)
-/* Return a list of all items in binKeeper that intersect range.
+/*
+ NOTE: Taken ~verbatim from kent source.
+ Return a list of all items in binKeeper that intersect range.
+
* Free this list with slFreeList. */
+
{
int startBin, endBin;
int i,j;
@@ -136,7 +143,6 @@ void BedFile::binKeeperFind(map<int, vector<BED>, std::less<int> > &bk, const in
{
for (vector<BED>::iterator el = bk[j].begin(); el != bk[j].end(); ++el) {
{
- //if (leftOf(end, el->start)) {break;}
if (overlaps(el->start, el->end, start, end) > 0)
{
hits.push_back(*el);
@@ -167,7 +173,6 @@ void BedFile::countHits(map<int, vector<BED>, std::less<int> > &bk, const int st
{
for (vector<BED>::iterator el = bk[j].begin(); el != bk[j].end(); ++el) {
{
- //if (leftOf(end, el->start)) {break;}
if (overlaps(el->start, el->end, start, end) > 0)
{
el->count++;
@@ -194,10 +199,10 @@ BedFile::~BedFile(void) {
bool BedFile::parseBedLine (BED &bed, const vector<string> &lineVector, const int &lineNum) {
-
+
if ((lineNum == 1) && (lineVector.size() >= 3)) {
this->bedType = lineVector.size();
-
+
if (this->bedType == 3) {
bed.chrom = lineVector[0];
bed.start = atoi(lineVector[1].c_str());
@@ -230,7 +235,7 @@ bool BedFile::parseBedLine (BED &bed, const vector<string> &lineVector, const in
}
}
else if ( (lineNum > 1) && (lineVector.size() == this->bedType)) {
-
+
if (this->bedType == 3) {
bed.chrom = lineVector[0];
bed.start = atoi(lineVector[1].c_str());
@@ -261,7 +266,7 @@ bool BedFile::parseBedLine (BED &bed, const vector<string> &lineVector, const in
bed.strand = lineVector[5];
return true;
}
-
+
if (bed.start > bed.end) {
cerr << "Error: malformed BED entry at line " << lineNum << ". Start was greater than End. Ignoring it and moving on." << endl;
return false;
@@ -271,12 +276,16 @@ bool BedFile::parseBedLine (BED &bed, const vector<string> &lineVector, const in
return false;
}
}
+ else if (lineVector.size() == 1) {
+ cerr << "Only one BED field detected: " << lineNum << ". Verify that your files are TAB-delimited. Exiting..." << endl;
+ exit(1);
+ }
else if (lineVector.size() != this->bedType) {
- cerr << "Differing number of BED fields encountered at line: " << lineNum << ". Exiting" << endl;
+ cerr << "Differing number of BED fields encountered at line: " << lineNum << ". Exiting..." << endl;
exit(1);
}
else if (lineVector.size() < 3) {
- cerr << "TAB delimited BED file with at least 3 fields (chrom, start, end) is required. Exiting" << endl;
+ cerr << "TAB delimited BED file with at least 3 fields (chrom, start, end) is required. Exiting..." << endl;
exit(1);
}
}
@@ -297,7 +306,7 @@ void BedFile::loadBedFileIntoMap() {
//while (bed >> bedEntry.chrom >> bedEntry.start >> bedEntry.end) {
while (getline(bed, bedLine)) {
-
+
vector<string> bedFields;
Tokenize(bedLine,bedFields);
@@ -314,7 +323,7 @@ void BedFile::loadBedFileIntoMap() {
void BedFile::loadBedFileIntoMapNoBin() {
// Are we dealing with a BED file or a BED passed via stdin?
-
+
// Case 1: Proper BED File.
if ( (this->bedFile != "") && (this->bedFile != "stdin") ) {
@@ -330,7 +339,7 @@ void BedFile::loadBedFileIntoMapNoBin() {
int lineNum = 0;
while (getline(bed, bedLine)) {
-
+
vector<string> bedFields;
Tokenize(bedLine,bedFields);
@@ -347,7 +356,7 @@ void BedFile::loadBedFileIntoMapNoBin() {
string bedLine;
BED bedEntry;
int lineNum = 0;
-
+
while (getline(cin, bedLine)) {
vector<string> bedFields;
diff --git a/src/utils/bedFile/bedFile.h b/src/utils/bedFile/bedFile.h
index bfc192f5cbc07fa2a678c1b472043f32587df165..285b4c47594cd2346c197cb6ffe0a61146058ce8 100755
--- a/src/utils/bedFile/bedFile.h
+++ b/src/utils/bedFile/bedFile.h
@@ -17,7 +17,7 @@ using namespace std;
//*************************************************
struct BED {
-
+
// UCSC BED fields
string chrom;
int start;
@@ -25,7 +25,7 @@ struct BED {
string name;
unsigned short score;
string strand;
-
+
// Additional fields
unsigned int count; // count of number of intervals
// that overlap this feature
@@ -83,29 +83,29 @@ public:
// Methods
bool parseBedLine (BED &, const vector<string> &, const int &);
- void loadBedFileIntoMap();
+ void loadBedFileIntoMap();
void loadBedFileIntoMapNoBin();
-
+
void binKeeperFind(map<int, vector<BED>,
- std::less<int> > &, const int,
- const int, vector<BED> &);
-
- void countHits(map<int, vector<BED>, std::less<int> > &, const int, const int);
-
+ std::less<int> > &, const int,
+ const int, vector<BED> &);
+
+ void countHits(map<int, vector<BED>, std::less<int> > &, const int, const int);
+
// a vector of the BED entries in the BED file.
vector<BED> bedVector;
masterBedMap bedMap;
masterBedMapNoBin bedMapNoBin;
-
+
map<string, int> minPosMap;
map<string, int> maxPosMap;
-
+
// the bedfile with which this instance is associated
string bedFile;
short bedType;
-
-private:
+private:
+ // none
};
#endif /* BEDFILE_H */