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bedFilePE.cpp 7.69 KiB
//
// bedFilePE.cpp
// BEDTools
//
// Created by Aaron Quinlan Spring 2009.
// Copyright 2009 Aaron Quinlan. All rights reserved.
//
// Summary: Contains common functions for finding BED overlaps.
//
// 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 "bedFilePE.h"
//***********************************************
// Common functions
//***********************************************
// Constructor
BedFilePE::BedFilePE(string &bedFile) {
this->bedFile = bedFile;
}
// Destructorc
BedFilePE::~BedFilePE(void) {
}
/*
reportBedPETab
Writes the _original_ BED entry for A.
Works for BEDPE only.
*/
void BedFilePE::reportBedPETab(const BEDPE &a) {
if (this->bedType == 6) {
printf("%s\t%d\t%d\t%s\t%d\t%d\t", a.chrom1.c_str(), a.start1, a.end1,
a.chrom2.c_str(), a.start2, a.end2);
}
else if (this->bedType == 7) {
printf("%s\t%d\t%d\t%s\t%d\t%d\t%s\t", a.chrom1.c_str(), a.start1, a.end1,
a.chrom2.c_str(), a.start2, a.end2,
a.name.c_str());
}
else if (this->bedType == 8) {
printf("%s\t%d\t%d\t%s\t%d\t%d\t%s\t%d\t", a.chrom1.c_str(), a.start1, a.end1,
a.chrom2.c_str(), a.start2, a.end2,
a.name.c_str(), a.score);
}
else if (this->bedType == 10) {
printf("%s\t%d\t%d\t%s\t%d\t%d\t%s\t%d\t%s\t%s\t", a.chrom1.c_str(), a.start1, a.end1,
a.chrom2.c_str(), a.start2, a.end2,
a.name.c_str(), a.score, a.strand1.c_str(), a.strand2.c_str());
}
}
/*
reportBedPENewLine
Writes the _original_ BED entry for A.
Works for BEDPE only.
*/
void BedFilePE::reportBedPENewLine(const BEDPE &a) {
if (this->bedType == 6) { printf("%s\t%d\t%d\t%s\t%d\t%d\n", a.chrom1.c_str(), a.start1, a.end1,
a.chrom2.c_str(), a.start2, a.end2);
}
else if (this->bedType == 7) {
printf("%s\t%d\t%d\t%s\t%d\t%d\t%s\n", a.chrom1.c_str(), a.start1, a.end1,
a.chrom2.c_str(), a.start2, a.end2,
a.name.c_str());
}
else if (this->bedType == 8) {
printf("%s\t%d\t%d\t%s\t%d\t%d\t%s\t%d\n", a.chrom1.c_str(), a.start1, a.end1,
a.chrom2.c_str(), a.start2, a.end2,
a.name.c_str(), a.score);
}
else if (this->bedType == 10) {
printf("%s\t%d\t%d\t%s\t%d\t%d\t%s\t%d\t%s\t%s\n", a.chrom1.c_str(), a.start1, a.end1,
a.chrom2.c_str(), a.start2, a.end2,
a.name.c_str(), a.score, a.strand1.c_str(), a.strand2.c_str());
}
}
bool BedFilePE::parseBedPELine (BEDPE &bed, const vector<string> &lineVector, const int &lineNum) {
if ((lineNum == 1) && (lineVector.size() >= 3)) {
this->bedType = lineVector.size();
if (this->bedType == 6) {
bed.chrom1 = lineVector[0];
bed.start1 = atoi(lineVector[1].c_str());
bed.end1 = atoi(lineVector[2].c_str());
bed.chrom2 = lineVector[3];
bed.start2 = atoi(lineVector[4].c_str());
bed.end2 = atoi(lineVector[5].c_str());
return true;
}
else if (this->bedType == 7) {
bed.chrom1 = lineVector[0];
bed.start1 = atoi(lineVector[1].c_str());
bed.end1 = atoi(lineVector[2].c_str());
bed.chrom2 = lineVector[3];
bed.start2 = atoi(lineVector[4].c_str());
bed.end2 = atoi(lineVector[5].c_str());
bed.name = lineVector[6];
return true;
}
else if (this->bedType == 8) {
bed.chrom1 = lineVector[0];
bed.start1 = atoi(lineVector[1].c_str());
bed.end1 = atoi(lineVector[2].c_str());
bed.chrom2 = lineVector[3];
bed.start2 = atoi(lineVector[4].c_str());
bed.end2 = atoi(lineVector[5].c_str());
bed.name = lineVector[6];
bed.score = atoi(lineVector[7].c_str());
return true;
}
else if (this->bedType == 10) {
bed.chrom1 = lineVector[0];
bed.start1 = atoi(lineVector[1].c_str());
bed.end1 = atoi(lineVector[2].c_str());
bed.chrom2 = lineVector[3]; bed.start2 = atoi(lineVector[4].c_str());
bed.end2 = atoi(lineVector[5].c_str());
bed.name = lineVector[6];
bed.score = atoi(lineVector[7].c_str());
bed.strand1 = lineVector[8];
bed.strand2 = lineVector[9];
return true;
}
else {
cerr << "Unexpected number of fields: " << lineNum << ". Verify that your files are TAB-delimited and that your BEDPE file has 6,7,8 or 10 fields. Exiting..." << endl;
exit(1);
}
if (bed.start1 > bed.end1) {
cerr << "Error: malformed BED entry at line " << lineNum << ". Start1 was greater than End1. Ignoring it and moving on." << endl;
return false;
}
else if (bed.start2 > bed.end2) {
cerr << "Error: malformed BED entry at line " << lineNum << ". Start2 was greater than End2. Ignoring it and moving on." << endl;
return false;
}
else if ( (bed.start1 < 0) || (bed.end1 < 0) || (bed.start2 < 0) || (bed.end2 < 0) ) {
cerr << "Error: malformed BED entry at line " << lineNum << ". Coordinate <= 0. Ignoring it and moving on." << endl;
return false;
}
}
else if ( (lineNum > 1) && (lineVector.size() == this->bedType)) {
if (this->bedType == 6) {
bed.chrom1 = lineVector[0];
bed.start1 = atoi(lineVector[1].c_str());
bed.end1 = atoi(lineVector[2].c_str());
bed.chrom2 = lineVector[3];
bed.start2 = atoi(lineVector[4].c_str());
bed.end2 = atoi(lineVector[5].c_str());
return true;
}
else if (this->bedType == 7) {
bed.chrom1 = lineVector[0];
bed.start1 = atoi(lineVector[1].c_str());
bed.end1 = atoi(lineVector[2].c_str());
bed.chrom2 = lineVector[3];
bed.start2 = atoi(lineVector[4].c_str());
bed.end2 = atoi(lineVector[5].c_str());
bed.name = lineVector[6];
return true;
}
else if (this->bedType == 8) {
bed.chrom1 = lineVector[0];
bed.start1 = atoi(lineVector[1].c_str());
bed.end1 = atoi(lineVector[2].c_str());
bed.chrom2 = lineVector[3];
bed.start2 = atoi(lineVector[4].c_str());
bed.end2 = atoi(lineVector[5].c_str());
bed.name = lineVector[6];
bed.score = atoi(lineVector[7].c_str());
return true;
}
else if (this->bedType == 10) {
bed.chrom1 = lineVector[0];
bed.start1 = atoi(lineVector[1].c_str()); bed.end1 = atoi(lineVector[2].c_str());
bed.chrom2 = lineVector[3];
bed.start2 = atoi(lineVector[4].c_str());
bed.end2 = atoi(lineVector[5].c_str());
bed.name = lineVector[6];
bed.score = atoi(lineVector[7].c_str());
bed.strand1 = lineVector[8];
bed.strand2 = lineVector[9];
return true;
}
else {
cerr << "Unexpected number of fields: " << lineNum << ". Verify that your files are TAB-delimited and that your BEDPE file has 6,7,8 or 10 fields. Exiting..." << endl;
exit(1);
}
if (bed.start1 > bed.end1) {
cerr << "Error: malformed BED entry at line " << lineNum << ". Start1 was greater than End1. Ignoring it and moving on." << endl;
return false;
}
else if (bed.start2 > bed.end2) {
cerr << "Error: malformed BED entry at line " << lineNum << ". Start2 was greater than End2. Ignoring it and moving on." << endl;
return false;
}
else if ( (bed.start1 < 0) || (bed.end1 < 0) || (bed.start2 < 0) || (bed.end2 < 0) ) {
cerr << "Error: malformed BED entry at line " << lineNum << ". Coordinate <= 0. Ignoring it and moving on." << endl;
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;
exit(1);
}
else if (lineVector.size() < 8) {
cerr << "TAB delimited BED file with 10 fields (chrom1, start1, end1, strand1, chrom2, start2, end2, strand2) is required. Exiting..." << endl;
exit(1);
}
return false;
}