diff --git a/src/mergeBed/mergeMain.cpp b/src/mergeBed/mergeMain.cpp
index 84b8db972337584ff7297d3058849a07776b5144..0a2f6946c6a20e540c75aaa5dbf3cd8bf3c1eb51 100755
--- a/src/mergeBed/mergeMain.cpp
+++ b/src/mergeBed/mergeMain.cpp
@@ -48,7 +48,7 @@ int main(int argc, char* argv[]) {
int parameterLength = (int)strlen(argv[i]);
- if(PARAMETER_CHECK("-i", 2, parameterLength)) {
+ if(PARAMETER_CHECK("-i", 2, parameterLength)) {
haveBed = true;
bedFile = argv[i + 1];
i++;
@@ -57,25 +57,25 @@ int main(int argc, char* argv[]) {
numEntries = true;
i++;
}
- else if(PARAMETER_CHECK("-d", 2, parameterLength)) {
- haveMaxDistance = true;
- maxDistance = atoi(argv[i + 1]);
- i++;
- }
+ else if(PARAMETER_CHECK("-d", 2, parameterLength)) {
+ haveMaxDistance = true;
+ maxDistance = atoi(argv[i + 1]);
+ i++;
+ }
else {
- cerr << 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) {
- cerr << endl << "*****" << endl << "*****ERROR: Need -i BED file. " << endl << "*****" << endl;
- showHelp = true;
+ cerr << endl << "*****" << endl << "*****ERROR: Need -i BED file. " << endl << "*****" << endl;
+ showHelp = true;
}
-
+
if (!showHelp) {
- BedMerge *bm = new BedMerge(bedFile, numEntries, maxDistance);
+ BedMerge *bm = new BedMerge(bedFile, numEntries, maxDistance);
bm->MergeBed();
return 0;
}
@@ -85,7 +85,7 @@ int main(int argc, char* argv[]) {
}
void ShowHelp(void) {
-
+
cerr << "===============================================" << endl;
cerr << " " <<PROGRAM_NAME << " v" << VERSION << endl ;
cerr << " Aaron Quinlan, Ph.D. (aaronquinlan@gmail.com) " << endl ;
@@ -94,7 +94,7 @@ void ShowHelp(void) {
cerr << "Description: Merges overlapping bed entries into a sinle interval." << endl << endl;
cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <input.bed>" << 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;
@@ -105,5 +105,5 @@ void ShowHelp(void) {
// end the program here
exit(1);
-
+
}
diff --git a/src/sortBed/sortBed.cpp b/src/sortBed/sortBed.cpp
index 90b6f2f970ef8f2858d0123aa5535126b8c95b27..13551e0f2ca38b5cc2ea5024f1626b0dd7fcaf71 100755
--- a/src/sortBed/sortBed.cpp
+++ b/src/sortBed/sortBed.cpp
@@ -24,9 +24,32 @@ BedSort::BedSort(string &bedFile) {
BedSort::~BedSort(void) {
}
-//
-// Merge overlapping BED entries into a single entry
-//
+
+/*
+ reportBed
+
+ Writes the _original_ BED entry for A.
+ Works for BED3 - BED6.
+*/
+void BedSort::reportBed(const BED &a) {
+
+ if (bed->bedType == 3) {
+ cout << a.chrom << "\t" << a.start << "\t" << a.end;
+ }
+ else if (bed->bedType == 4) {
+ cout << a.chrom << "\t" << a.start << "\t" << a.end << "\t"
+ << a.name;
+ }
+ else if (bed->bedType == 5) {
+ cout << a.chrom << "\t" << a.start << "\t" << a.end << "\t"
+ << a.name << "\t" << a.score;
+ }
+ else if (bed->bedType == 6) {
+ cout << a.chrom << "\t" << a.start << "\t" << a.end << "\t"
+ << a.name << "\t" << a.score << "\t" << a.strand;
+ }
+}
+
void BedSort::SortBed() {
// load the "B" bed file into a map so
@@ -40,8 +63,169 @@ void BedSort::SortBed() {
vector<BED> bedList = m->second;
for (unsigned int i = 0; i < bedList.size(); ++i) {
- cout << bedList[i].chrom << "\t" << bedList[i].start << "\t" << bedList[i].end << endl;
+ reportBed(bedList[i]); cout << "\n";
+ ///cout << bedList[i].chrom << "\t" << bedList[i].start << "\t" << bedList[i].end << endl;
+ }
+ }
+}
+
+
+void BedSort::SortBedBySizeAsc() {
+
+ // load the "B" bed file into a map so
+ // that we can easily compare "A" to it for overlaps
+ bed->loadBedFileIntoMapNoBin();
+
+ vector<BED> masterList;
+ masterList.reserve(1000000);
+
+ // loop through each chromosome and merge their BED entries
+ for (masterBedMapNoBin::iterator m = bed->bedMapNoBin.begin(); m != bed->bedMapNoBin.end(); ++m) {
+
+ // bedList is already sorted by start position.
+ vector<BED> bedList = m->second;
+
+ // add the entries from this chromosome to the current list
+ for (unsigned int i = 0; i < m->second.size(); ++i) {
+ masterList.push_back(m->second[i]);
}
}
+
+ // sort the master list by size (asc.)
+ sort(masterList.begin(), masterList.end(), sortBySizeAsc);
+
+ // report the entries in ascending order
+ for (unsigned int i = 0; i < masterList.size(); ++i) {
+ reportBed(masterList[i]); cout << "\n";
+ //cout << masterList[i].chrom << "\t" << masterList[i].start << "\t" << masterList[i].end << endl;
+ }
+}
+
+
+void BedSort::SortBedBySizeDesc() {
+
+ // load the "B" bed file into a map so
+ // that we can easily compare "A" to it for overlaps
+ bed->loadBedFileIntoMapNoBin();
+
+ vector<BED> masterList;
+ masterList.reserve(1000000);
+
+ // loop through each chromosome and merge their BED entries
+ for (masterBedMapNoBin::iterator m = bed->bedMapNoBin.begin(); m != bed->bedMapNoBin.end(); ++m) {
+
+ // bedList is already sorted by start position.
+ vector<BED> bedList = m->second;
+
+ // add the entries from this chromosome to the current list
+ for (unsigned int i = 0; i < m->second.size(); ++i) {
+ masterList.push_back(m->second[i]);
+ }
+ }
+
+ // sort the master list by size (asc.)
+ sort(masterList.begin(), masterList.end(), sortBySizeDesc);
+
+ // report the entries in ascending order
+ for (unsigned int i = 0; i < masterList.size(); ++i) {
+ reportBed(masterList[i]); cout << "\n";
+ //cout << masterList[i].chrom << "\t" << masterList[i].start << "\t" << masterList[i].end << endl;
+ }
+}
+
+void BedSort::SortBedByChromThenSizeAsc() {
+
+ // load the "B" bed file into a map so
+ // that we can easily compare "A" to it for overlaps
+ bed->loadBedFileIntoMapNoBin();
+
+ // loop through each chromosome and merge their BED entries
+ for (masterBedMapNoBin::iterator m = bed->bedMapNoBin.begin(); m != bed->bedMapNoBin.end(); ++m) {
+
+ // bedList is already sorted by start position.
+ vector<BED> bedList = m->second;
+ sort(bedList.begin(), bedList.end(), sortBySizeAsc);
+
+ for (unsigned int i = 0; i < bedList.size(); ++i) {
+ reportBed(bedList[i]); cout << "\n";
+ //cout << bedList[i].chrom << "\t" << bedList[i].start << "\t" << bedList[i].end << endl;
+ }
+ }
+}
+
+
+void BedSort::SortBedByChromThenSizeDesc() {
+
+ // load the "B" bed file into a map so
+ // that we can easily compare "A" to it for overlaps
+ bed->loadBedFileIntoMapNoBin();
+
+ // loop through each chromosome and merge their BED entries
+ for (masterBedMapNoBin::iterator m = bed->bedMapNoBin.begin(); m != bed->bedMapNoBin.end(); ++m) {
+
+ // bedList is already sorted by start position.
+ vector<BED> bedList = m->second;
+
+ sort(bedList.begin(), bedList.end(), sortBySizeDesc);
+
+ for (unsigned int i = 0; i < bedList.size(); ++i) {
+ reportBed(bedList[i]); cout << "\n";
+ //cout << bedList[i].chrom << "\t" << bedList[i].start << "\t" << bedList[i].end << endl;
+ }
+ }
+}
+
+
+void BedSort::SortBedByChromThenScoreAsc() {
+
+ // load the "B" bed file into a map so
+ // that we can easily compare "A" to it for overlaps
+ bed->loadBedFileIntoMapNoBin();
+
+ if (bed->bedType >= 5) {
+ // loop through each chromosome and merge their BED entries
+ for (masterBedMapNoBin::iterator m = bed->bedMapNoBin.begin(); m != bed->bedMapNoBin.end(); ++m) {
+
+ // bedList is already sorted by start position.
+ vector<BED> bedList = m->second;
+ sort(bedList.begin(), bedList.end(), sortByScoreAsc);
+
+ for (unsigned int i = 0; i < bedList.size(); ++i) {
+ reportBed(bedList[i]); cout << "\n";
+ //cout << bedList[i].chrom << "\t" << bedList[i].start << "\t" << bedList[i].end << endl;
+ }
+ }
+ }
+ else {
+ cerr << "Error: Requested a sort by score, but your BED file does not appear to be in BED 5 format or greater. Exiting." << endl;
+ exit(1);
+ }
+}
+
+
+void BedSort::SortBedByChromThenScoreDesc() {
+
+ // load the "B" bed file into a map so
+ // that we can easily compare "A" to it for overlaps
+ bed->loadBedFileIntoMapNoBin();
+
+ if (bed->bedType >= 5) {
+ // loop through each chromosome and merge their BED entries
+ for (masterBedMapNoBin::iterator m = bed->bedMapNoBin.begin(); m != bed->bedMapNoBin.end(); ++m) {
+
+ // bedList is already sorted by start position.
+ vector<BED> bedList = m->second;
+ sort(bedList.begin(), bedList.end(), sortByScoreDesc);
+
+ for (unsigned int i = 0; i < bedList.size(); ++i) {
+ reportBed(bedList[i]); cout << "\n";
+ //cout << bedList[i].chrom << "\t" << bedList[i].start << "\t" << bedList[i].end << endl;
+ }
+ }
+ }
+ else {
+ cerr << "Error: Requested a sort by score, but your BED file does not appear to be in BED 5 format or greater. Exiting." << endl;
+ exit(1);
+ }
}
diff --git a/src/sortBed/sortBed.h b/src/sortBed/sortBed.h
index 5e46e290a0760fd99fb033ddbeaaf07a14cb4718..7f3fcb3b1e168837aebe5329720260794ba7d703 100755
--- a/src/sortBed/sortBed.h
+++ b/src/sortBed/sortBed.h
@@ -22,16 +22,24 @@ class BedSort {
public:
- // constructor
- BedSort(string &);
-
- // destructor
- ~BedSort(void);
-
- void SortBed();
-
-private:
+ // constructor
+ BedSort(string &);
+
+ // destructor
+ ~BedSort(void);
+
+ // write BED to stdout
+ void reportBed(const BED &);
+
+ void SortBed(); // the default. sorts by chrom (asc.) then by start (asc.)
+ void SortBedBySizeAsc();
+ void SortBedBySizeDesc();
+ void SortBedByChromThenSizeAsc();
+ void SortBedByChromThenSizeDesc();
+ void SortBedByChromThenScoreAsc();
+ void SortBedByChromThenScoreDesc();
+private:
string bedFile;
// instance of a bed file class.
diff --git a/src/sortBed/sortMain.cpp b/src/sortBed/sortMain.cpp
index 362c60e8bb39c03d05fa9e7f915f7970a0a79918..e5d09f9c169dec895cadd98718edf4fdab6efbc6 100755
--- a/src/sortBed/sortMain.cpp
+++ b/src/sortBed/sortMain.cpp
@@ -23,7 +23,15 @@ int main(int argc, char* argv[]) {
// input files
string bedFile;
bool haveBed = false;
-
+ int sortChoices = 0;
+
+ bool sortBySizeAsc = false;
+ bool sortBySizeDesc = false;
+ bool sortByChromThenSizeAsc = false;
+ bool sortByChromThenSizeDesc = false;
+ bool sortByChromThenScoreAsc = false;
+ bool sortByChromThenScoreDesc = false;
+
for(int i = 1; i < argc; i++) {
int parameterLength = (int)strlen(argv[i]);
@@ -45,26 +53,82 @@ int main(int argc, char* argv[]) {
int parameterLength = (int)strlen(argv[i]);
- if(argv[i]) {
+ if(PARAMETER_CHECK("-i", 2, parameterLength)) {
haveBed = true;
- bedFile = argv[i];
+ bedFile = argv[i + 1];
+ i++;
+ }
+ else if(PARAMETER_CHECK("-sizeA", 6, parameterLength)) {
+ sortBySizeAsc = true;
+ sortChoices++;
+ i++;
+ }
+ else if(PARAMETER_CHECK("-sizeD", 6, parameterLength)) {
+ sortBySizeDesc = true;
+ sortChoices++;
+ i++;
+ }
+ else if(PARAMETER_CHECK("-chrThenSizeA", 13, parameterLength)) {
+ sortByChromThenSizeAsc = true;
+ sortChoices++;
i++;
}
+ else if(PARAMETER_CHECK("-chrThenSizeD", 13, parameterLength)) {
+ sortByChromThenSizeDesc = true;
+ sortChoices++;
+ i++;
+ }
+ else if(PARAMETER_CHECK("-chrThenScoreA", 14, parameterLength)) {
+ sortByChromThenScoreAsc = true;
+ sortChoices++;
+ i++;
+ }
+ else if(PARAMETER_CHECK("-chrThenScoreD", 14, parameterLength)) {
+ sortByChromThenScoreDesc = true;
+ sortChoices++;
+ i++;
+ }
else {
- cerr << 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) {
- cerr << endl << "*****" << endl << "*****ERROR: Need -i BED file. " << endl << "*****" << endl;
- showHelp = true;
+ cerr << endl << "*****" << endl << "*****ERROR: Need -i BED file. " << endl << "*****" << endl;
+ showHelp = true;
}
-
+ if (sortChoices > 1) {
+ cerr << endl << "*****" << endl << "*****ERROR: Sorting options are mutually exclusive. Please choose just one. " << endl << "*****" << endl;
+ showHelp = true;
+ }
+
+
if (!showHelp) {
BedSort *bm = new BedSort(bedFile);
- bm->SortBed();
+
+ if (sortBySizeAsc) {
+ bm->SortBedBySizeAsc();
+ }
+ else if (sortBySizeDesc) {
+ bm->SortBedBySizeDesc();
+ }
+ else if (sortByChromThenSizeAsc) {
+ bm->SortBedByChromThenSizeAsc();
+ }
+ else if (sortByChromThenSizeDesc) {
+ bm->SortBedByChromThenSizeDesc();
+ }
+ else if (sortByChromThenScoreAsc) {
+ bm->SortBedByChromThenScoreAsc();
+ }
+ else if (sortByChromThenScoreDesc) {
+ bm->SortBedByChromThenScoreDesc();
+ }
+ else {
+ bm->SortBed();
+ }
return 0;
}
else {
@@ -73,17 +137,27 @@ int main(int argc, char* argv[]) {
}
void ShowHelp(void) {
-
+
cerr << "===============================================" << endl;
cerr << " " <<PROGRAM_NAME << " v" << VERSION << endl ;
cerr << " Aaron Quinlan, Ph.D. (aaronquinlan@gmail.com) " << endl ;
cerr << " Hall Laboratory, 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;
+ cerr << "Description: Sorts a BED file in various and useful ways." << endl << endl;
+ cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <input.bed>" << endl << endl;
+
+ cerr << "OPTIONS: " << endl;
+ cerr << "\t" << "-sizeA\t\t" << "Sort the BED file by feature size in ascending order. Sorts across all chromosomes." << endl << endl;
+ cerr << "\t" << "-sizeD\t\t" << "Sort the BED file by feature size in descending order. Sorts across all chromosomes." << endl << endl;
+ cerr << "\t" << "-chrThenSizeA\t" << "Sort the BED file by chrom (ascending), then feature size in ascending order." << endl << endl;
+ cerr << "\t" << "-chrThenSizeD\t" << "Sort the BED file by chrom (ascending), then feature size in descending order." << endl << endl;
+ cerr << "\t" << "-chrThenScoreA\t" << "Sort the BED file by chrom (ascending), then score in ascending order." << endl << endl;
+ cerr << "\t" << "-chrThenScoreD\t" << "Sort the BED file by chrom (ascending), then scor size in descending order." << endl << endl;
+
+ cerr << "NOTES: " << endl;
+ cerr << "\t" << "-i stdin\t\t" << "Allows BED file A to be read from stdin. E.g.: cat a.bed | sortBed -i stdin" << endl << endl;
+ cerr << "\t***Only BED3 - BED6 formats allowed.***"<< endl << endl;
// end the program here
exit(1);
-
+
}
diff --git a/src/utils/bedFile/bedFile.cpp b/src/utils/bedFile/bedFile.cpp
index 67ac0cb37ca3462849d6e719d4e71f6c386bab32..19929909fc56f4e72d750c616359ad3d98f4cfc0 100755
--- a/src/utils/bedFile/bedFile.cpp
+++ b/src/utils/bedFile/bedFile.cpp
@@ -68,29 +68,6 @@ int max(const int a, int b) {
}
}
-//*********************************************
-// Sorting functions
-//*********************************************
-bool sortByChrom(BED const & a, BED const & b){
- if (a.chrom < b.chrom) return true;
- else return false;
-};
-
-bool sortByStart(const BED &a, const BED &b){
- if (a.start < b.start) return true;
- else return false;
-};
-
-bool byChromThenStart(BED const & a, BED const & b){
-
- if (a.chrom < b.chrom) return true;
- else if (a.chrom > b.chrom) return false;
-
- if (a.start < b.start) return true;
- else if (a.start >= b.start) return false;
-
-};
-
//************************************************
// Exception checking
//************************************************
@@ -120,7 +97,58 @@ static int getBin(int start, int end)
return 0;
}
+//*********************************************
+// Sorting functions
+//*********************************************
+bool sortByChrom(BED const & a, BED const & b){
+ if (a.chrom < b.chrom) return true;
+ else return false;
+};
+
+bool sortByStart(const BED &a, const BED &b){
+ if (a.start < b.start) return true;
+ else return false;
+};
+
+bool sortBySizeAsc(const BED &a, const BED &b){
+
+ unsigned int aLen = a.end - a.start;
+ unsigned int bLen = b.end - b.start;
+
+ if (aLen < bLen) return true;
+ else return false;
+};
+
+bool sortBySizeDesc(const BED &a, const BED &b){
+
+ unsigned int aLen = a.end - a.start;
+ unsigned int bLen = b.end - b.start;
+
+ if (aLen > bLen) return true;
+ else return false;
+};
+bool sortByScoreAsc(const BED &a, const BED &b){
+ if (a.score < b.score) return true;
+ else return false;
+};
+
+bool sortByScoreDesc(const BED &a, const BED &b){
+ if (a.score > b.score) return true;
+ else return false;
+};
+
+
+bool byChromThenStart(BED const & a, BED const & b){
+
+ if (a.chrom < b.chrom) return true;
+ else if (a.chrom > b.chrom) return false;
+
+ if (a.start < b.start) return true;
+ else if (a.start >= b.start) return false;
+
+ return false;
+};
void BedFile::binKeeperFind(map<int, vector<BED>, std::less<int> > &bk, const int start, const int end, vector<BED> &hits)
/*
diff --git a/src/utils/bedFile/bedFile.h b/src/utils/bedFile/bedFile.h
index 5f72330bb2ecd965e96520276f7d5439c7cdd73b..d0009798c5dbb8c3347b6eb43ae174816fc14490 100755
--- a/src/utils/bedFile/bedFile.h
+++ b/src/utils/bedFile/bedFile.h
@@ -59,6 +59,15 @@ std::string ToString(const T & value)
void Tokenize(const string& str, vector<string>& tokens);
+// BED Sorting Methods
+bool sortByChrom(BED const &, BED const &);
+bool sortByStart(const BED &, const BED &);
+bool sortBySizeAsc(const BED &, const BED &);
+bool sortBySizeDesc(const BED &, const BED &);
+bool sortByScoreAsc(const BED &, const BED &);
+bool sortByScoreDesc(const BED &, const BED &);
+bool byChromThenStart(BED const &, BED const &);
+
//*************************************************
// Common typedefs
//*************************************************