diff --git a/src/intersectBed/intersectBed.cpp b/src/intersectBed/intersectBed.cpp
index 1535703d96a8f9649014a82f58ffc2b15d8df161..1ad73134b2083aeb3855d73132776d23ca3f3a05 100644
--- a/src/intersectBed/intersectBed.cpp
+++ b/src/intersectBed/intersectBed.cpp
@@ -88,21 +88,11 @@ BedIntersect::BedIntersect(string bedAFile, string bedBFile, bool anyHit,
// create new BED file objects for A and B
_bedA = new BedFile(bedAFile);
_bedB = new BedFile(bedBFile);
-
- // dealing with a proper file
- if (_bedA->bedFile != "stdin") {
- if (_bamInput == false)
- IntersectBed();
- else
- IntersectBam(_bedA->bedFile);
- }
- // reading from stdin
- else {
- if (_bamInput == false)
- IntersectBed();
- else
- IntersectBam("stdin");
- }
+
+ if (_bamInput == false)
+ IntersectBed();
+ else
+ IntersectBam(bedAFile);
}
diff --git a/src/pairToBed/pairToBed.cpp b/src/pairToBed/pairToBed.cpp
index 5485f96c707f2dc1c5e7ed531e86f32c0f96fdce..4357d55d18a223aa645caa07f206fd96f8cbef19 100644
--- a/src/pairToBed/pairToBed.cpp
+++ b/src/pairToBed/pairToBed.cpp
@@ -33,35 +33,26 @@ bool IsCorrectMappingForBEDPE (const BamAlignment &bam) {
*/
BedIntersectPE::BedIntersectPE(string bedAFilePE, string bedBFile, float overlapFraction,
- string searchType, bool forceStrand, bool bamInput, bool bamOutput,
- bool useEditDistance) {
-
- _bedAFilePE = bedAFilePE;
- _bedBFile = bedBFile;
- _overlapFraction = overlapFraction;
- _forceStrand = forceStrand;
- _useEditDistance = useEditDistance;
- _searchType = searchType;
- _bamInput = bamInput;
- _bamOutput = bamOutput;
+ string searchType, bool forceStrand, bool bamInput,
+ bool bamOutput, bool uncompressedBam, bool useEditDistance) {
+
+ _bedAFilePE = bedAFilePE;
+ _bedBFile = bedBFile;
+ _overlapFraction = overlapFraction;
+ _forceStrand = forceStrand;
+ _useEditDistance = useEditDistance;
+ _searchType = searchType;
+ _bamInput = bamInput;
+ _bamOutput = bamOutput;
+ _isUncompressedBam = uncompressedBam;
_bedA = new BedFilePE(bedAFilePE);
_bedB = new BedFile(bedBFile);
- // dealing with a proper file
- if (_bedA->bedFile != "stdin") {
- if (_bamInput == false)
- IntersectBedPE();
- else
- IntersectBamPE(_bedA->bedFile);
- }
- // reading from stdin
- else {
- if (_bamInput == false)
- IntersectBedPE();
- else
- IntersectBamPE("stdin");
- }
+ if (_bamInput == false)
+ IntersectBedPE();
+ else
+ IntersectBamPE(_bedAFilePE);
}
@@ -396,7 +387,7 @@ void BedIntersectPE::IntersectBamPE(string bamFile) {
// open a BAM output to stdout if we are writing BAM
if (_bamOutput == true) {
// open our BAM writer
- writer.Open("stdout", header, refs);
+ writer.Open("stdout", header, refs, _isUncompressedBam);
}
// track the previous and current sequence
diff --git a/src/pairToBed/pairToBed.h b/src/pairToBed/pairToBed.h
index 68063c3484162c463cf0b042f965c286454c762a..0dd3910b3ed437db7c68772c4dab796d3ed0250b 100644
--- a/src/pairToBed/pairToBed.h
+++ b/src/pairToBed/pairToBed.h
@@ -43,7 +43,7 @@ public:
// constructor
BedIntersectPE(string bedAFilePE, string bedBFile, float overlapFraction,
- string searchType, bool forceStrand, bool bamInput, bool bamOutput, bool useEditDistance);
+ string searchType, bool forceStrand, bool bamInput, bool bamOutput, bool uncompressedBam, bool useEditDistance);
// destructor
~BedIntersectPE(void);
@@ -70,6 +70,7 @@ private:
bool _useEditDistance;
bool _bamInput;
bool _bamOutput;
+ bool _isUncompressedBam;
// instance of a paired-end bed file class.
BedFilePE *_bedA;
diff --git a/src/pairToBed/pairToBedMain.cpp b/src/pairToBed/pairToBedMain.cpp
index d50466fa00477d1d91e3cac35f972e01c545ab40..a26d3fe9c45eb929c201c55a00e055be40b52125 100644
--- a/src/pairToBed/pairToBedMain.cpp
+++ b/src/pairToBed/pairToBedMain.cpp
@@ -37,14 +37,15 @@ int main(int argc, char* argv[]) {
string searchType = "either";
// flags to track parameters
- bool haveBedA = false;
- bool haveBedB = false;
- bool haveSearchType = false;
- bool haveFraction = false;
- bool forceStrand = false;
- bool useEditDistance = false;
- bool inputIsBam = false;
- bool outputIsBam = true;
+ bool haveBedA = false;
+ bool haveBedB = false;
+ bool haveSearchType = false;
+ bool haveFraction = false;
+ bool forceStrand = false;
+ bool useEditDistance = false;
+ bool inputIsBam = false;
+ bool outputIsBam = true;
+ bool uncompressedBam = false;
// check to see if we should print out some help
if(argc <= 1) showHelp = true;
@@ -110,7 +111,10 @@ int main(int argc, char* argv[]) {
}
else if (PARAMETER_CHECK("-s", 2, parameterLength)) {
forceStrand = true;
- }
+ }
+ else if(PARAMETER_CHECK("-ubam", 5, parameterLength)) {
+ uncompressedBam = true;
+ }
else {
cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
showHelp = true;
@@ -146,7 +150,7 @@ int main(int argc, char* argv[]) {
BedIntersectPE *bi = new BedIntersectPE(bedAFile, bedBFile, overlapFraction,
searchType, forceStrand, inputIsBam,
- outputIsBam, useEditDistance);
+ outputIsBam, uncompressedBam, useEditDistance);
delete bi;
return 0;
}
diff --git a/src/windowBed/windowBed.cpp b/src/windowBed/windowBed.cpp
index dfd5622658659a3d7c5bd10bee7face9003041ce..65273c5325eb2de9212acc6e444dc60dab2d1635 100644
--- a/src/windowBed/windowBed.cpp
+++ b/src/windowBed/windowBed.cpp
@@ -38,20 +38,10 @@ BedWindow::BedWindow(string bedAFile, string bedBFile, int leftSlop, int rightSl
_bedA = new BedFile(bedAFile);
_bedB = new BedFile(bedBFile);
- // dealing with a proper file
- if (_bedA->bedFile != "stdin") {
- if (_bamInput == false)
- WindowIntersectBed();
- else
- WindowIntersectBam(_bedA->bedFile);
- }
- // reading from stdin
- else {
- if (_bamInput == false)
- WindowIntersectBed();
- else
- WindowIntersectBam("stdin");
- }
+ if (_bamInput == false)
+ WindowIntersectBed();
+ else
+ WindowIntersectBam(_bedAFile);
}
diff --git a/src/windowBed/windowMain.cpp b/src/windowBed/windowMain.cpp
index 7e0f7a4b867f98d6e20c93e3990e5dfd9a4e6e3f..5eb3465f8e00cd4dc13b1704232078041fb40531 100644
--- a/src/windowBed/windowMain.cpp
+++ b/src/windowBed/windowMain.cpp
@@ -34,21 +34,22 @@ int main(int argc, char* argv[]) {
string bedBFile;
// input arguments
- int leftSlop = 1000;
+ 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 matchOnStrand = false;
- bool inputIsBam = false;
- bool outputIsBam = true;
+ 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 matchOnStrand = false;
+ bool inputIsBam = false;
+ bool outputIsBam = true;
+ bool uncompressedBam = false;
// check to see if we should print out some help
if(argc <= 1) showHelp = true;
@@ -130,6 +131,9 @@ int main(int argc, char* argv[]) {
rightSlop = atoi(argv[i + 1]);
i++;
}
+ }
+ else if(PARAMETER_CHECK("-ubam", 5, parameterLength)) {
+ uncompressedBam = true;
}
else {
cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
@@ -175,7 +179,8 @@ int main(int argc, char* argv[]) {
if (!showHelp) {
BedWindow *bi = new BedWindow(bedAFile, bedBFile, leftSlop, rightSlop, anyHit,
- noHit, writeCount, strandWindows, matchOnStrand, inputIsBam, outputIsBam);
+ noHit, writeCount, strandWindows, matchOnStrand,
+ inputIsBam, outputIsBam, uncompressedBam);
delete bi;
return 0;
}
@@ -200,6 +205,8 @@ void ShowHelp(void) {
cerr << "Options: " << endl;
cerr << "\t-abam\t" << "The A input file is in BAM format. Output will be BAM as well." << endl << endl;
+
+ cerr << "\t-ubam\t" << "Write uncompressed BAM output. Default is to write compressed BAM." << endl << endl;
cerr << "\t-bed\t" << "When using BAM input (-abam), write output as BED. The default" << endl;
cerr << "\t\tis to write output in BAM when using -abam." << endl << endl;