diff --git a/src/closestBed/closestBed.cpp b/src/closestBed/closestBed.cpp
index 046db2077c98ca89c0961accd25221032c0f7957..735e2a9ebfe3a8012592c58a30c61dc3827e3370 100644
--- a/src/closestBed/closestBed.cpp
+++ b/src/closestBed/closestBed.cpp
@@ -23,7 +23,7 @@ const int SLOPGROWTH = 2048000;
*/
BedClosest::BedClosest(string &bedAFile, string &bedBFile, bool sameStrand, bool diffStrand,
string &tieMode, bool reportDistance, bool signDistance, string &_strandedDistMode,
- bool ignoreOverlaps)
+ bool ignoreOverlaps, bool printHeader)
: _bedAFile(bedAFile)
, _bedBFile(bedBFile)
, _tieMode(tieMode)
@@ -33,6 +33,7 @@ BedClosest::BedClosest(string &bedAFile, string &bedBFile, bool sameStrand, bool
, _signDistance(signDistance)
, _strandedDistMode(_strandedDistMode)
, _ignoreOverlaps(ignoreOverlaps)
+ , _printHeader(printHeader)
{
_bedA = new BedFile(_bedAFile);
_bedB = new BedFile(_bedBFile);
@@ -220,6 +221,10 @@ void BedClosest::FindClosestBed() {
BedLineStatus bedStatus;
_bedA->Open();
+ // report A's header first if asked.
+ if (_printHeader == true) {
+ _bedA->PrintHeader();
+ }
// process each entry in A in search of the closest feature in B
while ((bedStatus = _bedA->GetNextBed(a, lineNum)) != BED_INVALID) {
if (bedStatus == BED_VALID) {
diff --git a/src/closestBed/closestBed.h b/src/closestBed/closestBed.h
index 82bd9b40b5fc6f6c2de1d246502f586f5ccdf923..8190dec93ee25443cb85c9a8a10a71547851d28a 100644
--- a/src/closestBed/closestBed.h
+++ b/src/closestBed/closestBed.h
@@ -30,7 +30,7 @@ public:
BedClosest(string &bedAFile, string &bedBFile,
bool sameStrand, bool diffStrand, string &tieMode,
bool reportDistance, bool signDistance, string &strandedDistMode,
- bool ignoreOverlaps);
+ bool ignoreOverlaps, bool printHeader);
// destructor
~BedClosest(void);
@@ -50,6 +50,7 @@ private:
bool _signDistance;
string _strandedDistMode;
bool _ignoreOverlaps;
+ bool _printHeader;
BedFile *_bedA, *_bedB;
diff --git a/src/closestBed/closestMain.cpp b/src/closestBed/closestMain.cpp
index 8b34a70743ef21688f3ed2067ca7da1c001d501c..0128af24fc6edbb4fa20558e56a1b541774be9b1 100644
--- a/src/closestBed/closestMain.cpp
+++ b/src/closestBed/closestMain.cpp
@@ -43,6 +43,7 @@ int main(int argc, char* argv[]) {
bool reportDistance = false;
bool signDistance = false;
bool haveStrandedDistMode = false;
+ bool printHeader = false;
// check to see if we should print out some help
@@ -106,6 +107,9 @@ int main(int argc, char* argv[]) {
i++;
}
}
+ else if(PARAMETER_CHECK("-header", 7, parameterLength)) {
+ printHeader = true;
+ }
else {
cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
showHelp = true;
@@ -136,7 +140,9 @@ int main(int argc, char* argv[]) {
}
if (!showHelp) {
- BedClosest *bc = new BedClosest(bedAFile, bedBFile, sameStrand, diffStrand, tieMode, reportDistance, signDistance, strandedDistMode, ignoreOverlaps);
+ BedClosest *bc = new BedClosest(bedAFile, bedBFile, sameStrand,
+ diffStrand, tieMode, reportDistance,
+ signDistance, strandedDistMode, ignoreOverlaps, printHeader);
delete bc;
return 0;
}
@@ -191,6 +197,8 @@ void ShowHelp(void) {
cerr << "\t\t- \"all\" Report all ties (default)." << endl;
cerr << "\t\t- \"first\" Report the first tie that occurred in the B file." << endl;
cerr << "\t\t- \"last\" Report the last tie that occurred in the B file." << endl << endl;
+
+ cerr << "\t-header\t" << "Print the header from the A file prior to results." << endl << endl;
cerr << "Notes: " << endl;
cerr << "\tReports \"none\" for chrom and \"-1\" for all other fields when a feature" << endl;
diff --git a/src/flankBed/flankBed.cpp b/src/flankBed/flankBed.cpp
index 33ff711b5c8ad5377a518c746bd1f10e8d9604f2..f7e12495120281194aa38f5c22aa1695bb2e83a7 100644
--- a/src/flankBed/flankBed.cpp
+++ b/src/flankBed/flankBed.cpp
@@ -13,14 +13,18 @@
#include "flankBed.h"
-BedFlank::BedFlank(string &bedFile, string &genomeFile, bool forceStrand, float leftFlank, float rightFlank, bool fractional) {
+BedFlank::BedFlank(string &bedFile, string &genomeFile, bool forceStrand,
+ float leftFlank, float rightFlank, bool fractional,
+ bool printHeader)
+{
_bedFile = bedFile;
_genomeFile = genomeFile;
_forceStrand = forceStrand;
_leftFlank = leftFlank;
_rightFlank = rightFlank;
- _fractional = fractional;
+ _fractional = fractional;
+ _printHeader = printHeader;
_bed = new BedFile(bedFile);
_genome = new GenomeFile(genomeFile);
@@ -42,6 +46,11 @@ void BedFlank::FlankBed() {
BedLineStatus bedStatus;
_bed->Open();
+ // report A's header first if asked.
+ if (_printHeader == true) {
+ _bed->PrintHeader();
+ }
+
bedStatus = _bed->GetNextBed(bedEntry, lineNum);
while (bedStatus != BED_INVALID) {
if (bedStatus == BED_VALID) {
diff --git a/src/flankBed/flankBed.h b/src/flankBed/flankBed.h
index a77326a80637d6602b007447d4b15dd6df068e41..f344f60f18686f84f796618a4ad1659a52430189 100644
--- a/src/flankBed/flankBed.h
+++ b/src/flankBed/flankBed.h
@@ -30,7 +30,9 @@ class BedFlank {
public:
// constructor
- BedFlank(string &bedFile, string &genomeFile, bool forceStrand, float leftSlop, float rightSlop, bool fractional);
+ BedFlank(string &bedFile, string &genomeFile, bool forceStrand,
+ float leftSlop, float rightSlop, bool fractional,
+ bool printHeader);
// destructor
~BedFlank(void);
@@ -46,6 +48,7 @@ private:
float _leftFlank;
float _rightFlank;
bool _fractional;
+ bool _printHeader;
BedFile *_bed;
GenomeFile *_genome;
diff --git a/src/flankBed/flankBedMain.cpp b/src/flankBed/flankBedMain.cpp
index 107db20e044e3d63b898a12a7805d7545338d51e..062839e6a377298ce849bd209ea5d9e093df46f5 100644
--- a/src/flankBed/flankBedMain.cpp
+++ b/src/flankBed/flankBedMain.cpp
@@ -43,6 +43,7 @@ int main(int argc, char* argv[]) {
float leftSlop = 0.0;
float rightSlop = 0.0;
bool fractional = false;
+ bool printHeader = false;
for(int i = 1; i < argc; i++) {
int parameterLength = (int)strlen(argv[i]);
@@ -101,6 +102,9 @@ int main(int argc, char* argv[]) {
else if(PARAMETER_CHECK("-pct", 4, parameterLength)) {
fractional = true;
}
+ else if(PARAMETER_CHECK("-header", 7, parameterLength)) {
+ printHeader = true;
+ }
else {
cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
showHelp = true;
@@ -126,7 +130,8 @@ int main(int argc, char* argv[]) {
}
if (!showHelp) {
- BedFlank *bc = new BedFlank(bedFile, genomeFile, forceStrand, leftSlop, rightSlop, fractional);
+ BedFlank *bc = new BedFlank(bedFile, genomeFile, forceStrand,
+ leftSlop, rightSlop, fractional, printHeader);
delete bc;
return 0;
@@ -163,6 +168,8 @@ void ShowHelp(void) {
cerr << "\t-pct\t" << "Define -l and -r as a fraction of the feature's length." << endl;
cerr << "\t\tE.g. if used on a 1000bp feature, -l 0.50, " << endl;
cerr << "\t\twill add 500 bp \"upstream\". Default = false." << endl << endl;
+
+ cerr << "\t-header\t" << "Print the header from the input file prior to results." << endl << endl;
cerr << "Notes: " << endl;
cerr << "\t(1) Starts will be set to 0 if options would force it below 0." << endl;
diff --git a/src/slopBed/slopBed.cpp b/src/slopBed/slopBed.cpp
index be9e37687c14f1e21cd626d24525dc43b65bf764..68eda5a2859aa7760aae8341d04f330865e45f87 100644
--- a/src/slopBed/slopBed.cpp
+++ b/src/slopBed/slopBed.cpp
@@ -13,14 +13,17 @@
#include "slopBed.h"
-BedSlop::BedSlop(string &bedFile, string &genomeFile, bool forceStrand, float leftSlop, float rightSlop, bool fractional) {
+BedSlop::BedSlop(string &bedFile, string &genomeFile, bool forceStrand,
+ float leftSlop, float rightSlop, bool fractional,
+ bool printHeader) {
_bedFile = bedFile;
_genomeFile = genomeFile;
_forceStrand = forceStrand;
_leftSlop = leftSlop;
_rightSlop = rightSlop;
- _fractional = fractional;
+ _fractional = fractional;
+ _printHeader = printHeader;
_bed = new BedFile(bedFile);
_genome = new GenomeFile(genomeFile);
@@ -42,6 +45,11 @@ void BedSlop::SlopBed() {
BedLineStatus bedStatus;
_bed->Open();
+ // report header first if asked.
+ if (_printHeader == true) {
+ _bed->PrintHeader();
+ }
+
bedStatus = _bed->GetNextBed(bedEntry, lineNum);
while (bedStatus != BED_INVALID) {
if (bedStatus == BED_VALID) {
diff --git a/src/slopBed/slopBed.h b/src/slopBed/slopBed.h
index d22590c729a8da7c6241b07636dac784d3ed6e23..7de0afd728cce49b85f31f0ec60c1f2efbcd4001 100644
--- a/src/slopBed/slopBed.h
+++ b/src/slopBed/slopBed.h
@@ -30,7 +30,8 @@ class BedSlop {
public:
// constructor
- BedSlop(string &bedFile, string &genomeFile, bool forceStrand, float leftSlop, float rightSlop, bool fractional);
+ BedSlop(string &bedFile, string &genomeFile, bool forceStrand,
+ float leftSlop, float rightSlop, bool fractional, bool printHeader);
// destructor
~BedSlop(void);
@@ -46,6 +47,7 @@ private:
float _leftSlop;
float _rightSlop;
bool _fractional;
+ bool _printHeader;
BedFile *_bed;
GenomeFile *_genome;
diff --git a/src/slopBed/slopBedMain.cpp b/src/slopBed/slopBedMain.cpp
index 01e0164908b49cb981498ca9753e156b5f51697f..b5f148e56dc6aab8aa714a1f7cc45ba8f01ded44 100644
--- a/src/slopBed/slopBedMain.cpp
+++ b/src/slopBed/slopBedMain.cpp
@@ -43,6 +43,7 @@ int main(int argc, char* argv[]) {
float leftSlop = 0.0;
float rightSlop = 0.0;
bool fractional = false;
+ bool printHeader = false;
for(int i = 1; i < argc; i++) {
int parameterLength = (int)strlen(argv[i]);
@@ -101,6 +102,9 @@ int main(int argc, char* argv[]) {
else if(PARAMETER_CHECK("-pct", 4, parameterLength)) {
fractional = true;
}
+ else if(PARAMETER_CHECK("-header", 7, parameterLength)) {
+ printHeader = true;
+ }
else {
cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
showHelp = true;
@@ -126,7 +130,7 @@ int main(int argc, char* argv[]) {
}
if (!showHelp) {
- BedSlop *bc = new BedSlop(bedFile, genomeFile, forceStrand, leftSlop, rightSlop, fractional);
+ BedSlop *bc = new BedSlop(bedFile, genomeFile, forceStrand, leftSlop, rightSlop, fractional, printHeader);
delete bc;
return 0;
@@ -164,6 +168,8 @@ void ShowHelp(void) {
cerr << "\t\tE.g. if used on a 1000bp feature, -l 0.50, " << endl;
cerr << "\t\twill add 500 bp \"upstream\". Default = false." << endl << endl;
+ cerr << "\t-header\t" << "Print the header from the input file prior to results." << endl << endl;
+
cerr << "Notes: " << endl;
cerr << "\t(1) Starts will be set to 0 if options would force it below 0." << endl;
cerr << "\t(2) Ends will be set to the chromosome length if requested slop would" << endl;
diff --git a/src/windowBed/windowBed.cpp b/src/windowBed/windowBed.cpp
index 513d91fef05c5cbc0a59d00f05d611d1b6a9bd88..b93ea4ae8fef38753f00afff61b6cb6acf03a008 100644
--- a/src/windowBed/windowBed.cpp
+++ b/src/windowBed/windowBed.cpp
@@ -18,7 +18,8 @@
*/
BedWindow::BedWindow(string bedAFile, string bedBFile, int leftSlop, int rightSlop,
bool anyHit, bool noHit, bool writeCount, bool strandWindows,
- bool matchOnSameStrand, bool matchOnDiffStrand, bool bamInput, bool bamOutput, bool isUncompressedBam) {
+ bool matchOnSameStrand, bool matchOnDiffStrand, bool bamInput,
+ bool bamOutput, bool isUncompressedBam, bool printHeader) {
_bedAFile = bedAFile;
_bedBFile = bedBFile;
@@ -35,6 +36,7 @@ BedWindow::BedWindow(string bedAFile, string bedBFile, int leftSlop, int rightSl
_bamInput = bamInput;
_bamOutput = bamOutput;
_isUncompressedBam = isUncompressedBam;
+ _printHeader = printHeader;
_bedA = new BedFile(bedAFile);
_bedB = new BedFile(bedBFile);
@@ -133,6 +135,10 @@ void BedWindow::WindowIntersectBed() {
hits.reserve(100);
_bedA->Open();
+ // report A's header first if asked.
+ if (_printHeader == true) {
+ _bedA->PrintHeader();
+ }
while ((bedStatus = _bedA->GetNextBed(a, lineNum)) != BED_INVALID) {
if (bedStatus == BED_VALID) {
FindWindowOverlaps(a, hits);
diff --git a/src/windowBed/windowBed.h b/src/windowBed/windowBed.h
index 84f1b1b1e9e4fa576be0cd35198699f56d499481..31c8a076c43c14c8ada993df96d94e1c9741226e 100644
--- a/src/windowBed/windowBed.h
+++ b/src/windowBed/windowBed.h
@@ -34,7 +34,8 @@ public:
// constructor
BedWindow(string bedAFile, string bedBFile, int leftSlop, int rightSlop,
bool anyHit, bool noHit, bool writeCount, bool strandWindows,
- bool matchOnSameStrand, bool matchOnDiffStrand, bool bamInput, bool bamOutput, bool isUncompressedBam);
+ bool matchOnSameStrand, bool matchOnDiffStrand, bool bamInput,
+ bool bamOutput, bool isUncompressedBam, bool printHeader);
// destructor
~BedWindow(void);
@@ -53,7 +54,8 @@ private:
bool _matchOnDiffStrand;
bool _bamInput;
bool _bamOutput;
- bool _isUncompressedBam;
+ bool _isUncompressedBam;
+ bool _printHeader;
// instance of a bed file class.
BedFile *_bedA, *_bedB;
diff --git a/src/windowBed/windowMain.cpp b/src/windowBed/windowMain.cpp
index 7d70f3a4359951b233cf83b31e8f1812390f8a1f..cbb5739a14120596893da0d89c26e34a78809249 100644
--- a/src/windowBed/windowMain.cpp
+++ b/src/windowBed/windowMain.cpp
@@ -37,20 +37,21 @@ int main(int argc, char* argv[]) {
int leftSlop = 1000;
int rightSlop = 1000;
- bool haveBedA = false;
- bool haveBedB = false;
- bool noHit = false;
- bool anyHit = false;
- bool writeCount = false;
- bool haveSlop = false;
- bool haveLeft = false;
- bool haveRight = false;
- bool strandWindows = false;
+ bool haveBedA = false;
+ bool haveBedB = false;
+ bool noHit = false;
+ bool anyHit = false;
+ bool writeCount = false;
+ bool haveSlop = false;
+ bool haveLeft = false;
+ bool haveRight = false;
+ bool strandWindows = false;
bool matchOnSameStrand = false;
bool matchOnDiffStrand = false;
- bool inputIsBam = false;
- bool outputIsBam = true;
- bool uncompressedBam = false;
+ bool inputIsBam = false;
+ bool outputIsBam = true;
+ bool uncompressedBam = false;
+ bool printHeader = false;
// check to see if we should print out some help
if(argc <= 1) showHelp = true;
@@ -139,6 +140,9 @@ int main(int argc, char* argv[]) {
else if(PARAMETER_CHECK("-ubam", 5, parameterLength)) {
uncompressedBam = true;
}
+ else if(PARAMETER_CHECK("-header", 7, parameterLength)) {
+ printHeader = true;
+ }
else {
cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
showHelp = true;
@@ -189,7 +193,7 @@ int main(int argc, char* argv[]) {
if (!showHelp) {
BedWindow *bi = new BedWindow(bedAFile, bedBFile, leftSlop, rightSlop, anyHit,
noHit, writeCount, strandWindows, matchOnSameStrand, matchOnDiffStrand,
- inputIsBam, outputIsBam, uncompressedBam);
+ inputIsBam, outputIsBam, uncompressedBam, printHeader);
delete bi;
return 0;
}
@@ -257,6 +261,8 @@ void ShowHelp(void) {
cerr << "\t-v\t" << "Only report those entries in A that have _no overlaps_ with B." << endl;
cerr << "\t\t- Similar to \"grep -v.\"" << endl << endl;
+
+ cerr << "\t-header\t" << "Print the header from the A file prior to results." << endl << endl;
// end the program here
exit(1);