Added -header to sortBed

src/sortBed/sortBed.cpp

@@ -15,9 +15,15 @@
 //
 // Constructor
 //
-BedSort::BedSort(string &bedFile) {
+BedSort::BedSort(string &bedFile, bool printHeader) {
     _bedFile = bedFile;
     _bed = new BedFile(bedFile);
+    
+    _bed->loadBedFileIntoMapNoBin();
+    // report the header first if asked.
+    if (printHeader == true) {
+        _bed->PrintHeader();
+    }
 }
 
 //
@@ -29,10 +35,6 @@ BedSort::~BedSort(void) {
 
 void BedSort::SortBed() {
 
-    // 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) {
 
@@ -48,10 +50,6 @@ void BedSort::SortBed() {
 
 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);
 
@@ -79,10 +77,6 @@ void BedSort::SortBedBySizeAsc() {
 
 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);
 
@@ -109,10 +103,6 @@ void BedSort::SortBedBySizeDesc() {
 
 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) {
 
@@ -129,10 +119,6 @@ void BedSort::SortBedByChromThenSizeAsc() {
 
 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) {
 
@@ -150,10 +136,6 @@ void BedSort::SortBedByChromThenSizeDesc() {
 
 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) {
@@ -176,10 +158,6 @@ void BedSort::SortBedByChromThenScoreAsc() {
 
 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) {

src/sortBed/sortBed.h

@@ -26,7 +26,7 @@ class BedSort {
 public:
 
     // constructor
-    BedSort(string &);
+    BedSort(string &bedFile, bool printHeader);
 
     // destructor
     ~BedSort(void);
@@ -44,7 +44,4 @@ private:
 
     // instance of a bed file class.
     BedFile *_bed;
-
-    // methods
-
 };

src/sortBed/sortMain.cpp

@@ -40,7 +40,7 @@ int main(int argc, char* argv[]) {
     bool sortByChromThenSizeDesc  = false;
     bool sortByChromThenScoreAsc  = false;
     bool sortByChromThenScoreDesc = false;
-
+    bool printHeader        = false;
 
     for(int i = 1; i < argc; i++) {
         int parameterLength = (int)strlen(argv[i]);
@@ -88,6 +88,9 @@ int main(int argc, char* argv[]) {
             sortByChromThenScoreDesc = true;
             sortChoices++;
         }
+        else if(PARAMETER_CHECK("-header", 7, parameterLength)) {
+            printHeader = true;
+        }
         else {
             cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
             showHelp = true;
@@ -106,7 +109,7 @@ int main(int argc, char* argv[]) {
 
 
     if (!showHelp) {
-        BedSort *bm = new BedSort(bedFile);
+        BedSort *bm = new BedSort(bedFile, printHeader);
 
         if (sortBySizeAsc) {
             bm->SortBedBySizeAsc();
@@ -150,7 +153,9 @@ void ShowHelp(void) {
     cerr << "\t" << "-chrThenSizeA\t"   << "Sort by chrom (asc), then feature size (asc)." << endl;
     cerr << "\t" << "-chrThenSizeD\t"   << "Sort by chrom (asc), then feature size (desc)." << endl;
     cerr << "\t" << "-chrThenScoreA\t"  << "Sort by chrom (asc), then score (asc)." << endl;
-    cerr << "\t" << "-chrThenScoreD\t"  << "Sort by chrom (asc), then score (desc)." << endl << endl;
+    cerr << "\t" << "-chrThenScoreD\t"  << "Sort by chrom (asc), then score (desc)." << endl;
+
+    cerr << "\t-header\t"       << "Print the header from the A file prior to results." << endl << endl;
 
     exit(1);