diff --git a/src/complementBed/complementMain.cpp b/src/complementBed/complementMain.cpp
index 8a900426f62121a940d90064431adf63ecf36abf..f70f6c9bfd24ca1babdccccdb183f0afbeb3a15a 100755
--- a/src/complementBed/complementMain.cpp
+++ b/src/complementBed/complementMain.cpp
@@ -57,14 +57,14 @@ int main(int argc, char* argv[]) {
i++;
}
else {
- cout << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
+ cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
showHelp = true;
}
}
// make sure we have both input files
if (!haveBed || !haveGenome) {
- cout << endl << "*****" << endl << "*****ERROR: Need -i BED file and -g Genome file. " << endl << "*****" << endl;
+ cerr << endl << "*****" << endl << "*****ERROR: Need -i BED file and -g Genome file. " << endl << "*****" << endl;
showHelp = true;
}
if (!showHelp) {
@@ -79,23 +79,23 @@ int main(int argc, char* argv[]) {
void ShowHelp(void) {
- cout << "=======================================================" << endl;
- cout << PROGRAM_NAME << " v" << VERSION << endl ;
- cout << "Aaron Quinlan, Ph.D." << endl;
- cout << "aaronquinlan@gmail.com" << endl ;
- cout << "Hall Laboratory" << endl;
- cout << "Biochemistry and Molecular Genetics" << endl;
- cout << "University of Virginia" << endl;
- cout << "=======================================================" << endl << endl;
- cout << "Description: Returns the base pair complement of a BED file." << endl << endl;
- cout << "***NOTE: Only BED3 - BED6 formats allowed.***"<< endl << endl;
-
- cout << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <input.bed>" << endl << endl;
+ cerr << "=======================================================" << endl;
+ cerr << PROGRAM_NAME << " v" << VERSION << endl ;
+ cerr << "Aaron Quinlan, Ph.D." << endl;
+ cerr << "aaronquinlan@gmail.com" << endl ;
+ cerr << "Hall Laboratory" << endl;
+ cerr << "Biochemistry and Molecular Genetics" << endl;
+ cerr << "University of Virginia" << endl;
+ cerr << "=======================================================" << endl << endl;
+ cerr << "Description: Returns the base pair complement of a BED file." << endl << endl;
+ cerr << "***NOTE: Only BED3 - BED6 formats allowed.***"<< endl << endl;
+
+ cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <input.bed>" << endl << endl;
- //cout << "OPTIONS: " << endl;
- //cout << "\t" << "-n\t\t\t" << "Report the number of BED entries that were merged. (=1 if no merging occured)" << endl;
- //cout << "\t" << "-d\t\t\t" << "Maximum distance between features that will be merged. (Default is 0)" << endl;
- //cout << "\t\t\t\t" << "For example, \"-d 50\" will merge features that are <= 50 bp apart." << endl << endl;
+ //cerr << "OPTIONS: " << endl;
+ //cerr << "\t" << "-n\t\t\t" << "Report the number of BED entries that were merged. (=1 if no merging occured)" << endl;
+ //cerr << "\t" << "-d\t\t\t" << "Maximum distance between features that will be merged. (Default is 0)" << endl;
+ //cerr << "\t\t\t\t" << "For example, \"-d 50\" will merge features that are <= 50 bp apart." << endl << endl;
// end the program here
exit(1);
diff --git a/src/coverageBed/coverageMain.cpp b/src/coverageBed/coverageMain.cpp
index a5b9912aa3f3b1d57059be7ac02ea3de208fd34b..5630bdc313b1f8545aa6599ac44f5aaa174c084c 100755
--- a/src/coverageBed/coverageMain.cpp
+++ b/src/coverageBed/coverageMain.cpp
@@ -56,14 +56,14 @@ int main(int argc, char* argv[]) {
i++;
}
else {
- cout << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
+ cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
showHelp = true;
}
}
// make sure we have both input files
if (!haveBedA || !haveBedB) {
- cout << endl << "*****" << endl << "*****ERROR: Need -a and -b files. " << endl << "*****" << endl;
+ cerr << endl << "*****" << endl << "*****ERROR: Need -a and -b files. " << endl << "*****" << endl;
showHelp = true;
}
@@ -80,25 +80,25 @@ int main(int argc, char* argv[]) {
void ShowHelp(void) {
- cout << "=======================================================" << endl;
- cout << PROGRAM_NAME << " v" << VERSION << endl ;
- cout << "Aaron Quinlan, Ph.D." << endl;
- cout << "aaronquinlan@gmail.com" << endl ;
- cout << "Hall Laboratory" << endl;
- cout << "Biochemistry and Molecular Genetics" << endl;
- cout << "University of Virginia" << endl;
- cout << "=======================================================" << endl << endl;
- //cout << "Description: Reportoverlaps between a.bed and b.bed." << endl << endl;
- cout << "***NOTE: Only BED3 - BED6 formats allowed.***"<< endl << endl;
-
- cout << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <a.bed> -b <b.bed>" << endl << endl;
-
- //cout << "OPTIONS: " << endl;
- //cout << "\t" << "-u\t\t\t" << "Write ORIGINAL a.bed entry ONCE if ANY overlap bed." << endl << "\t\t\t\tIn other words, ignore multiple overlaps." << endl << endl;
- //cout << "\t" << "-v \t\t\t" << "Only report those entries in A that have NO OVERLAP in B." << endl << "\t\t\t\tSimilar to grep -v." << endl << endl;
- //cout << "\t" << "-f (e.g. 0.05)\t\t" << "Minimum overlap req'd as fraction of a.bed." << endl << "\t\t\t\tDefault is 1E-9 (effectively 1bp)." << endl << endl;
- //cout << "\t" << "-c \t\t\t" << "For each entry in A, report the number of hits in B while restricting to -f." << endl << "\t\t\t\tReports 0 for A entries that have no overlap with B." << endl << endl;
- //cout << "\t" << "-wb \t\t\t" << "Write the entry in B for each overlap." << endl << "\t\t\t\tUseful for knowing _what_ A overlaps. Restricted by -f." << endl << endl;
+ cerr << "=======================================================" << endl;
+ cerr << PROGRAM_NAME << " v" << VERSION << endl ;
+ cerr << "Aaron Quinlan, Ph.D." << endl;
+ cerr << "aaronquinlan@gmail.com" << endl ;
+ cerr << "Hall Laboratory" << endl;
+ cerr << "Biochemistry and Molecular Genetics" << endl;
+ cerr << "University of Virginia" << endl;
+ cerr << "=======================================================" << endl << endl;
+ //cerr << "Description: Reportoverlaps between a.bed and b.bed." << endl << endl;
+ cerr << "***NOTE: Only BED3 - BED6 formats allowed.***"<< endl << endl;
+
+ cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <a.bed> -b <b.bed>" << endl << endl;
+
+ //cerr << "OPTIONS: " << endl;
+ //cerr << "\t" << "-u\t\t\t" << "Write ORIGINAL a.bed entry ONCE if ANY overlap bed." << endl << "\t\t\t\tIn other words, ignore multiple overlaps." << endl << endl;
+ //cerr << "\t" << "-v \t\t\t" << "Only report those entries in A that have NO OVERLAP in B." << endl << "\t\t\t\tSimilar to grep -v." << endl << endl;
+ //cerr << "\t" << "-f (e.g. 0.05)\t\t" << "Minimum overlap req'd as fraction of a.bed." << endl << "\t\t\t\tDefault is 1E-9 (effectively 1bp)." << endl << endl;
+ //cerr << "\t" << "-c \t\t\t" << "For each entry in A, report the number of hits in B while restricting to -f." << endl << "\t\t\t\tReports 0 for A entries that have no overlap with B." << endl << endl;
+ //cerr << "\t" << "-wb \t\t\t" << "Write the entry in B for each overlap." << endl << "\t\t\t\tUseful for knowing _what_ A overlaps. Restricted by -f." << endl << endl;
// end the program here
exit(1);
diff --git a/src/fastaFromBed/fastaFromBedMain.cpp b/src/fastaFromBed/fastaFromBedMain.cpp
index 6aec35e4d5832a8c0221ac5e81150b12f154ba48..490a6c371360cf83a68ce837d9e5b1be64c47975 100755
--- a/src/fastaFromBed/fastaFromBedMain.cpp
+++ b/src/fastaFromBed/fastaFromBedMain.cpp
@@ -71,7 +71,7 @@ int main(int argc, char* argv[]) {
i++;
}
else {
- cout << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
+ cerr << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
showHelp = true;
}
}
@@ -84,7 +84,7 @@ int main(int argc, char* argv[]) {
Bed2Fa *b2f = new Bed2Fa(useNameOnly, fastaDbFile, bedFile, fastaOutFile);
- cout << PROGRAM_NAME << " completed." << endl;
+ cerr << PROGRAM_NAME << " completed." << endl;
return 0;
}
else {
@@ -94,27 +94,27 @@ int main(int argc, char* argv[]) {
void ShowHelp(void) {
- cout << "=======================================================" << endl;
- cout << PROGRAM_NAME << " v" << VERSION << endl << endl;
- cout << "Aaron Quinlan, Ph.D." << endl;
- cout << "aaronquinlan@gmail.com" << endl << endl;
- cout << "Hall Laboratory" << endl;
- cout << "Biochemistry and Molecular Genetics" << endl;
- cout << "University of Virginia" << endl;
- cout << "=======================================================" << endl << endl;
- cout << "Description: Extract DNA sequences into a fasta file based on BED coordinates." << endl << endl;
-
- cout << "Usage: " << PROGRAM_NAME << " -db <fasta db file> -bed <bed coordinates file> -fo <output fasta file w/ requested DNA>" << endl << endl;
-
- cout << "Input Files:" << endl;
- cout << " -db <FASTA db file> " << endl;
- cout << " -bed <BED coordinates file> " << endl;
-
- cout << "Output Files:" << endl;
- cout << " -fo <FASTA output file> " << endl;
-
- cout << "\nHelp:" << endl;
- cout << " -h shows this help text" << endl;
+ cerr << "=======================================================" << endl;
+ cerr << PROGRAM_NAME << " v" << VERSION << endl << endl;
+ cerr << "Aaron Quinlan, Ph.D." << endl;
+ cerr << "aaronquinlan@gmail.com" << endl << endl;
+ cerr << "Hall Laboratory" << endl;
+ cerr << "Biochemistry and Molecular Genetics" << endl;
+ cerr << "University of Virginia" << endl;
+ cerr << "=======================================================" << endl << endl;
+ cerr << "Description: Extract DNA sequences into a fasta file based on BED coordinates." << endl << endl;
+
+ cerr << "Usage: " << PROGRAM_NAME << " -db <fasta db file> -bed <bed coordinates file> -fo <output fasta file w/ requested DNA>" << endl << endl;
+
+ cerr << "Input Files:" << endl;
+ cerr << " -db <FASTA db file> " << endl;
+ cerr << " -bed <BED coordinates file> " << endl;
+
+ cerr << "Output Files:" << endl;
+ cerr << " -fo <FASTA output file> " << endl;
+
+ cerr << "\nHelp:" << endl;
+ cerr << " -h shows this help text" << endl;
// end the program here
exit(1);
diff --git a/src/genomeCoverageBed/genomeCoverageMain.cpp b/src/genomeCoverageBed/genomeCoverageMain.cpp
index 2b6be564786e3693dc009e2864a5d4d6867655d1..794e7458d2e7bb3e241162a749ae54ec0d3845a9 100755
--- a/src/genomeCoverageBed/genomeCoverageMain.cpp
+++ b/src/genomeCoverageBed/genomeCoverageMain.cpp
@@ -72,14 +72,14 @@ int main(int argc, char* argv[]) {
i++;
}
else {
- cout << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
+ cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
showHelp = true;
}
}
// make sure we have both input files
if (!haveBed || !haveGenome) {
- cout << endl << "*****" << endl << "*****ERROR: Need both a BED (-i) and a genome ()-g) file. " << endl << "*****" << endl;
+ cerr << endl << "*****" << endl << "*****ERROR: Need both a BED (-i) and a genome (-g) file. " << endl << "*****" << endl;
showHelp = true;
}
@@ -97,32 +97,32 @@ int main(int argc, char* argv[]) {
void ShowHelp(void) {
- cout << "=======================================================" << endl;
- cout << PROGRAM_NAME << " v" << VERSION << endl ;
- cout << "Aaron Quinlan, Ph.D." << endl;
- cout << "aaronquinlan@gmail.com" << endl ;
- cout << "Hall Laboratory" << endl;
- cout << "Biochemistry and Molecular Genetics" << endl;
- cout << "University of Virginia" << endl;
- cout << "=======================================================" << endl << endl;
- cout << "Description: Compute the coverage of a BED (-i) file on genome (-g) file." << endl << endl;
- cout << "***NOTE: Only BED3 - BED6 formats allowed.***"<< endl << endl;
-
- cout << "Usage: " << PROGRAM_NAME << " [OPTIONS] -g <genome> -i <bed>" << endl << endl;
+ cerr << "=======================================================" << endl;
+ cerr << PROGRAM_NAME << " v" << VERSION << endl ;
+ cerr << "Aaron Quinlan, Ph.D." << endl;
+ cerr << "aaronquinlan@gmail.com" << endl ;
+ cerr << "Hall Laboratory" << endl;
+ cerr << "Biochemistry and Molecular Genetics" << endl;
+ cerr << "University of Virginia" << endl;
+ cerr << "=======================================================" << endl << endl;
+ cerr << "Description: Compute the coverage of a BED (-i) file on genome (-g) file." << endl << endl;
+ cerr << "***NOTE: Only BED3 - BED6 formats allowed.***"<< endl << endl;
+
+ cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -g <genome> -i <bed>" << endl << endl;
- cout << "OPTIONS: " << endl;
- cout << "\t" << "-d\t\t\t" << "Report the depth at each genome position." << endl << "\t\t\t\tDefault behavior is to report a histogram." << endl << endl;
- cout << "\t" << "-s \t\t\t" << "Report depth based on start sites." << endl << endl;
- cout << "\t" << "-max\t\t\t" << "Combine all positions with a depth > max into a single bin in the histogram." << endl << endl;
- cout << "NOTES: " << endl;
- cout << "\tThe genome file should tab delimited and structured as follows: <chr><TAB><size>. For example, Mus musculus:" << endl;
- cout << "\tchr1\t197195432" << endl;
- cout << "\tchr2\t181748087" << endl;
- cout << "\t..." << endl;
- cout << "\tchrY_random\t58682461" << endl << endl;
- cout << "TIPS:" << endl;
- cout << "\tOne can use the UCSC Genome Browser's MySQL database to extract chromosome sizes. For example, H. sapiens:" << endl << endl;
- cout << "\tmysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \"select chrom, size from hg18.chromInfo\" > hg18.genome"
+ cerr << "OPTIONS: " << endl;
+ cerr << "\t" << "-d\t\t\t" << "Report the depth at each genome position." << endl << "\t\t\t\tDefault behavior is to report a histogram." << endl << endl;
+ cerr << "\t" << "-s \t\t\t" << "Report depth based on start sites." << endl << endl;
+ cerr << "\t" << "-max\t\t\t" << "Combine all positions with a depth > max into a single bin in the histogram." << endl << endl;
+ cerr << "NOTES: " << endl;
+ cerr << "\tThe genome file should tab delimited and structured as follows: <chr><TAB><size>. For example, Mus musculus:" << endl;
+ cerr << "\tchr1\t197195432" << endl;
+ cerr << "\tchr2\t181748087" << endl;
+ cerr << "\t..." << endl;
+ cerr << "\tchrY_random\t58682461" << endl << endl;
+ cerr << "TIPS:" << endl;
+ cerr << "\tOne can use the UCSC Genome Browser's MySQL database to extract chromosome sizes. For example, H. sapiens:" << endl << endl;
+ cerr << "\tmysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \"select chrom, size from hg18.chromInfo\" > hg18.genome"
<< endl << endl;
// end the program here
exit(1);
diff --git a/src/intersectBed/intersectMain.cpp b/src/intersectBed/intersectMain.cpp
index 2936b9fdadf0e9e8c206d6b8feb7630f0526a3a8..894d0273202d54b59cb2c13479581ba8c70ae9d2 100755
--- a/src/intersectBed/intersectMain.cpp
+++ b/src/intersectBed/intersectMain.cpp
@@ -83,24 +83,24 @@ int main(int argc, char* argv[]) {
i++;
}
else {
- cout << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
+ cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
showHelp = true;
}
}
// make sure we have both input files
if (!haveBedA || !haveBedB) {
- cout << endl << "*****" << endl << "*****ERROR: Need -a and -b files. " << endl << "*****" << endl;
+ cerr << endl << "*****" << endl << "*****ERROR: Need -a and -b files. " << endl << "*****" << endl;
showHelp = true;
}
if (anyHit && noHit) {
- cout << endl << "*****" << endl << "*****ERROR: Request either -u OR -v, not both." << endl << "*****" << endl;
+ cerr << endl << "*****" << endl << "*****ERROR: Request either -u OR -v, not both." << endl << "*****" << endl;
showHelp = true;
}
if (writeB && writeCount) {
- cout << endl << "*****" << endl << "*****ERROR: Request either -wb OR -c, not both." << endl << "*****" << endl;
+ cerr << endl << "*****" << endl << "*****ERROR: Request either -wb OR -c, not both." << endl << "*****" << endl;
showHelp = true;
}
@@ -117,25 +117,25 @@ int main(int argc, char* argv[]) {
void ShowHelp(void) {
- cout << "=======================================================" << endl;
- cout << PROGRAM_NAME << " v" << VERSION << endl ;
- cout << "Aaron Quinlan, Ph.D." << endl;
- cout << "aaronquinlan@gmail.com" << endl ;
- cout << "Hall Laboratory" << endl;
- cout << "Biochemistry and Molecular Genetics" << endl;
- cout << "University of Virginia" << endl;
- cout << "=======================================================" << endl << endl;
- cout << "Description: Report overlaps between a.bed and b.bed." << endl << endl;
- cout << "***NOTE: Only BED3 - BED6 formats allowed.***"<< endl << endl;
-
- cout << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <a.bed> -b <b.bed>" << endl << endl;
-
- cout << "OPTIONS: " << endl;
- cout << "\t" << "-u\t\t\t" << "Write ORIGINAL a.bed entry ONCE if ANY overlap bed." << endl << "\t\t\t\tIn other words, ignore multiple overlaps." << endl << endl;
- cout << "\t" << "-v \t\t\t" << "Only report those entries in A that have NO OVERLAP in B." << endl << "\t\t\t\tSimilar to grep -v." << endl << endl;
- cout << "\t" << "-f (e.g. 0.05)\t\t" << "Minimum overlap req'd as fraction of a.bed." << endl << "\t\t\t\tDefault is 1E-9 (effectively 1bp)." << endl << endl;
- cout << "\t" << "-c \t\t\t" << "For each entry in A, report the number of hits in B while restricting to -f." << endl << "\t\t\t\tReports 0 for A entries that have no overlap with B." << endl << endl;
- cout << "\t" << "-wb \t\t\t" << "Write the entry in B for each overlap." << endl << "\t\t\t\tUseful for knowing _what_ A overlaps. Restricted by -f." << endl << endl;
+ cerr << "=======================================================" << endl;
+ cerr << PROGRAM_NAME << " v" << VERSION << endl ;
+ cerr << "Aaron Quinlan, Ph.D." << endl;
+ cerr << "aaronquinlan@gmail.com" << endl ;
+ cerr << "Hall Laboratory" << endl;
+ cerr << "Biochemistry and Molecular Genetics" << endl;
+ cerr << "University of Virginia" << endl;
+ cerr << "=======================================================" << endl << endl;
+ cerr << "Description: Report overlaps between a.bed and b.bed." << endl << endl;
+ cerr << "***NOTE: Only BED3 - BED6 formats allowed.***"<< endl << endl;
+
+ cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <a.bed> -b <b.bed>" << endl << endl;
+
+ cerr << "OPTIONS: " << endl;
+ cerr << "\t" << "-u\t\t\t" << "Write ORIGINAL a.bed entry ONCE if ANY overlap bed." << endl << "\t\t\t\tIn other words, ignore multiple overlaps." << endl << endl;
+ cerr << "\t" << "-v \t\t\t" << "Only report those entries in A that have NO OVERLAP in B." << endl << "\t\t\t\tSimilar to grep -v." << endl << endl;
+ cerr << "\t" << "-f (e.g. 0.05)\t\t" << "Minimum overlap req'd as fraction of a.bed." << endl << "\t\t\t\tDefault is 1E-9 (effectively 1bp)." << endl << endl;
+ cerr << "\t" << "-c \t\t\t" << "For each entry in A, report the number of hits in B while restricting to -f." << endl << "\t\t\t\tReports 0 for A entries that have no overlap with B." << endl << endl;
+ cerr << "\t" << "-wb \t\t\t" << "Write the entry in B for each overlap." << endl << "\t\t\t\tUseful for knowing _what_ A overlaps. Restricted by -f." << endl << endl;
// end the program here
exit(1);
diff --git a/src/mergeBed/mergeMain.cpp b/src/mergeBed/mergeMain.cpp
index 17a5f02f9d9d03130804e1d57327689fdd323ea7..08e712235833325f7a9170eed6b780cfbd47c5eb 100755
--- a/src/mergeBed/mergeMain.cpp
+++ b/src/mergeBed/mergeMain.cpp
@@ -63,14 +63,14 @@ int main(int argc, char* argv[]) {
i++;
}
else {
- cout << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
+ cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
showHelp = true;
}
}
// make sure we have both input files
if (!haveBed) {
- cout << endl << "*****" << endl << "*****ERROR: Need -i BED file. " << endl << "*****" << endl;
+ cerr << endl << "*****" << endl << "*****ERROR: Need -i BED file. " << endl << "*****" << endl;
showHelp = true;
}
@@ -86,22 +86,22 @@ int main(int argc, char* argv[]) {
void ShowHelp(void) {
- cout << "=======================================================" << endl;
- cout << PROGRAM_NAME << " v" << VERSION << endl ;
- cout << "Aaron Quinlan, Ph.D." << endl;
- cout << "aaronquinlan@gmail.com" << endl ;
- cout << "Hall Laboratory" << endl;
- cout << "Biochemistry and Molecular Genetics" << endl;
- cout << "University of Virginia" << endl;
- cout << "=======================================================" << endl << endl;
- cout << "Description: Merges overlapping bed entries into a sinle interval." << endl << endl;
- cout << "***NOTE: Only BED3 - BED6 formats allowed.***"<< endl << endl;
-
- cout << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <input.bed>" << endl << endl;
+ cerr << "=======================================================" << endl;
+ cerr << PROGRAM_NAME << " v" << VERSION << endl ;
+ cerr << "Aaron Quinlan, Ph.D." << endl;
+ cerr << "aaronquinlan@gmail.com" << endl ;
+ cerr << "Hall Laboratory" << endl;
+ cerr << "Biochemistry and Molecular Genetics" << endl;
+ cerr << "University of Virginia" << endl;
+ cerr << "=======================================================" << endl << endl;
+ cerr << "Description: Merges overlapping bed entries into a sinle interval." << endl << endl;
+ cerr << "***NOTE: Only BED3 - BED6 formats allowed.***"<< endl << endl;
+
+ cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <input.bed>" << endl << endl;
- cout << "OPTIONS: " << endl;
- cout << "\t" << "-n\t\t\t" << "Report the number of BED entries that were merged. (=1 if no merging occured)" << endl << endl;
- cout << "\t" << "-d\t\t\t" << "Maximum distance between features allowed for features to be merged. (Default=0)" << endl << endl;
+ cerr << "OPTIONS: " << endl;
+ cerr << "\t" << "-n\t\t\t" << "Report the number of BED entries that were merged. (=1 if no merging occured)" << endl << endl;
+ cerr << "\t" << "-d\t\t\t" << "Maximum distance between features allowed for features to be merged. (Default=0)" << endl << endl;
// end the program here
exit(1);
diff --git a/src/sortBed/sortMain.cpp b/src/sortBed/sortMain.cpp
index 00e32f95d9defc390d6c6948d5c29ac520d60fb6..021097ee6dd9631e81ba62edfc44e4b222256cfd 100755
--- a/src/sortBed/sortMain.cpp
+++ b/src/sortBed/sortMain.cpp
@@ -51,14 +51,14 @@ int main(int argc, char* argv[]) {
i++;
}
else {
- cout << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
+ cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
showHelp = true;
}
}
// make sure we have both input files
if (!haveBed) {
- cout << endl << "*****" << endl << "*****ERROR: Need -i BED file. " << endl << "*****" << endl;
+ cerr << endl << "*****" << endl << "*****ERROR: Need -i BED file. " << endl << "*****" << endl;
showHelp = true;
}
@@ -74,18 +74,18 @@ int main(int argc, char* argv[]) {
void ShowHelp(void) {
- cout << "=======================================================" << endl;
- cout << PROGRAM_NAME << " v" << VERSION << endl ;
- cout << "Aaron Quinlan, Ph.D." << endl;
- cout << "aaronquinlan@gmail.com" << endl ;
- cout << "Hall Laboratory" << endl;
- cout << "Biochemistry and Molecular Genetics" << endl;
- cout << "University of Virginia" << endl;
- cout << "=======================================================" << endl << endl;
- cout << "Description: Sorts a BED file by chrom, then by start position." << endl << endl;
- cout << "***NOTE: Only BED3 - BED6 formats allowed.***"<< endl << endl;
-
- cout << "Usage: " << PROGRAM_NAME << " <input.bed>" << endl << endl;
+ cerr << "=======================================================" << endl;
+ cerr << PROGRAM_NAME << " v" << VERSION << endl ;
+ cerr << "Aaron Quinlan, Ph.D." << endl;
+ cerr << "aaronquinlan@gmail.com" << endl ;
+ cerr << "Hall Laboratory" << endl;
+ cerr << "Biochemistry and Molecular Genetics" << endl;
+ cerr << "University of Virginia" << endl;
+ cerr << "=======================================================" << endl << endl;
+ cerr << "Description: Sorts a BED file by chrom, then by start position." << endl << endl;
+ cerr << "***NOTE: Only BED3 - BED6 formats allowed.***"<< endl << endl;
+
+ cerr << "Usage: " << PROGRAM_NAME << " <input.bed>" << endl << endl;
// end the program here
exit(1);
diff --git a/src/utils/bedFile/bedFile.cpp b/src/utils/bedFile/bedFile.cpp
index cc7550a9baee5e940ea3394c273f71cc0a8f074e..8766e3cfe79df0b61926ae7a7fce3a570586e7f5 100755
--- a/src/utils/bedFile/bedFile.cpp
+++ b/src/utils/bedFile/bedFile.cpp
@@ -248,11 +248,11 @@ bool BedFile::parseBedLine (BED &bed, const vector<string> &lineVector, const in
}
if (bed.start > bed.end) {
- cout << "Error: malformed BED entry at line " << lineNum << ". Start was greater than End. Ignoring it and moving on." << endl;
+ cerr << "Error: malformed BED entry at line " << lineNum << ". Start was greater than End. Ignoring it and moving on." << endl;
return false;
}
else if ( (bed.start < 0) || (bed.end < 0) ) {
- cout << "Error: malformed BED entry at line " << lineNum << ". Coordinate <= 0. Ignoring it and moving on." << endl;
+ cerr << "Error: malformed BED entry at line " << lineNum << ". Coordinate <= 0. Ignoring it and moving on." << endl;
return false;
}
}