Issue #50. SlopBed now adds percent-based slop to features with the -pct option.

src/slopBed/slopBed.cpp

@@ -7,24 +7,25 @@
   University of Virginia
   aaronquinlan@gmail.com
 
-  Licenced under the GNU General Public License 2.0 license.
+  Licensed under the GNU General Public License 2.0 license.
 ******************************************************************************/
 #include "lineFileUtilities.h"
 #include "slopBed.h"
 
 
-BedSlop::BedSlop(string &bedFile, string &genomeFile, bool &forceStrand, int &leftSlop, int &rightSlop) {
+BedSlop::BedSlop(string &bedFile, string &genomeFile, bool forceStrand, float leftSlop, float rightSlop, bool fractional) {
 
     _bedFile     = bedFile;
     _genomeFile  = genomeFile;
     _forceStrand = forceStrand;
-
-    _leftSlop  = leftSlop;
-    _rightSlop = rightSlop;
+    _leftSlop    = leftSlop;
+    _rightSlop   = rightSlop;
+    _fractional  = fractional; 
 
     _bed    = new BedFile(bedFile);
     _genome = new GenomeFile(genomeFile);
 
+    // get going, slop it up.
     SlopBed();
 }
 
@@ -44,7 +45,14 @@ void BedSlop::SlopBed() {
     bedStatus = _bed->GetNextBed(bedEntry, lineNum);
     while (bedStatus != BED_INVALID) {
         if (bedStatus == BED_VALID) {
-            AddSlop(bedEntry);
+            if (_fractional == false) {
+                AddSlop(bedEntry, _leftSlop, _rightSlop);
+            }
+            else {
+                int leftSlop  = (int) (_leftSlop  * bedEntry.size());
+                int rightSlop = (int) (_rightSlop * bedEntry.size());
+                AddSlop(bedEntry, leftSlop, rightSlop);
+            }
             _bed->reportBedNewLine(bedEntry);
             bedEntry = nullBed;
         }
@@ -54,7 +62,7 @@ void BedSlop::SlopBed() {
 }
 
 
-void BedSlop::AddSlop(BED &bed) {
+void BedSlop::AddSlop(BED &bed, int leftSlop, int rightSlop) {
 
     // special handling if the BED entry is on the negative
     // strand and the user cares about strandedness.
@@ -62,20 +70,20 @@ void BedSlop::AddSlop(BED &bed) {
 
     if ( (_forceStrand) && (bed.strand == "-") ) {
         // inspect the start
-        if ( (static_cast<int>(bed.start) - _rightSlop) > 0 ) bed.start -= _rightSlop;
+        if ( (static_cast<int>(bed.start) - rightSlop) > 0 ) bed.start -= rightSlop;
         else bed.start = 0;
 
         // inspect the start
-        if ( (static_cast<int>(bed.end) + _leftSlop) <= static_cast<int>(chromSize)) bed.end += _leftSlop;
+        if ( (static_cast<int>(bed.end) + leftSlop) <= static_cast<int>(chromSize)) bed.end += leftSlop;
         else bed.end = chromSize;
     }
     else {
         // inspect the start
-        if ( (static_cast<int>(bed.start) - _leftSlop) > 0) bed.start -= _leftSlop;
+        if ( (static_cast<int>(bed.start) - leftSlop) > 0) bed.start -= leftSlop;
         else bed.start = 0;
 
         // inspect the end
-        if ( (static_cast<int>(bed.end) + _rightSlop) <= static_cast<int>(chromSize)) bed.end += _rightSlop;
+        if ( (static_cast<int>(bed.end) + rightSlop) <= static_cast<int>(chromSize)) bed.end += rightSlop;
         else bed.end = chromSize;
     }
 }

src/slopBed/slopBed.h

@@ -30,7 +30,7 @@ class BedSlop {
 public:
 
     // constructor
-    BedSlop(string &bedFile, string &genomeFile, bool &forceStrand, int &leftSlop, int &rightSlop) ;
+    BedSlop(string &bedFile, string &genomeFile, bool forceStrand, float leftSlop, float rightSlop, bool fractional);
 
     // destructor
     ~BedSlop(void);
@@ -42,9 +42,10 @@ private:
     string _bedFile;
     string _genomeFile;
 
-    bool _forceStrand;
-    int _leftSlop;
-    int _rightSlop;
+    bool   _forceStrand;
+    float  _leftSlop;
+    float  _rightSlop;
+    bool   _fractional;
 
     BedFile *_bed;
     GenomeFile *_genome;
@@ -54,5 +55,5 @@ private:
     void SlopBed();
 
     // method to add requested "slop" to a single BED entry
-    void AddSlop(BED &bed);
+    void AddSlop(BED &bed, int leftSlop, int rightSlop);
 };

src/slopBed/slopBedMain.cpp

@@ -40,8 +40,9 @@ int main(int argc, char* argv[]) {
     bool haveBoth   = false;
 
     bool forceStrand = false;
-    int leftSlop = 0;
-    int rightSlop = 0;
+    float leftSlop   = 0.0;
+    float rightSlop  = 0.0;
+    bool  fractional = false;
 
     for(int i = 1; i < argc; i++) {
         int parameterLength = (int)strlen(argv[i]);
@@ -75,28 +76,31 @@ int main(int argc, char* argv[]) {
         else if(PARAMETER_CHECK("-l", 2, parameterLength)) {
             if ((i+1) < argc) {
                 haveLeft = true;
-                leftSlop = atoi(argv[i + 1]);
+                leftSlop = atof(argv[i + 1]);
                 i++;
             }
         }
         else if(PARAMETER_CHECK("-r", 2, parameterLength)) {
             if ((i+1) < argc) {
                 haveRight = true;
-                rightSlop = atoi(argv[i + 1]);
+                rightSlop = atof(argv[i + 1]);
                 i++;
             }
         }
         else if(PARAMETER_CHECK("-b", 2, parameterLength)) {
             if ((i+1) < argc) {
                 haveBoth = true;
-                leftSlop = atoi(argv[i + 1]);
-                rightSlop = atoi(argv[i + 1]);
+                leftSlop = atof(argv[i + 1]);
+                rightSlop = atof(argv[i + 1]);
                 i++;
             }
         }
         else if(PARAMETER_CHECK("-s", 2, parameterLength)) {
             forceStrand = true;
         }
+        else if(PARAMETER_CHECK("-pct", 4, parameterLength)) {
+            fractional = true;
+        }
         else {
           cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
             showHelp = true;
@@ -122,7 +126,7 @@ int main(int argc, char* argv[]) {
     }
 
     if (!showHelp) {
-        BedSlop *bc = new BedSlop(bedFile, genomeFile, forceStrand, leftSlop, rightSlop);
+        BedSlop *bc = new BedSlop(bedFile, genomeFile, forceStrand, leftSlop, rightSlop, fractional);
         delete bc;
 
         return 0;
@@ -144,18 +148,22 @@ void ShowHelp(void) {
 
     cerr << "Options: " << endl;
     cerr << "\t-b\t"                << "Increase the BED/GFF/VCF entry by -b base pairs in each direction." << endl;
-    cerr                            << "\t\t- (Integer)" << endl;
+    cerr                            << "\t\t- (Integer) or (Float, e.g. 0.1) if used with -pct." << endl << endl;
 
     cerr << "\t-l\t"                << "The number of base pairs to subtract from the start coordinate." << endl;
-    cerr                            << "\t\t- (Integer)" << endl;
-
+    cerr                            << "\t\t- (Integer) or (Float, e.g. 0.1) if used with -pct." << endl << endl;
+        
     cerr << "\t-r\t"                << "The number of base pairs to add to the end coordinate." << endl;
-    cerr                            << "\t\t- (Integer)" << endl;
-
+    cerr                            << "\t\t- (Integer) or (Float, e.g. 0.1) if used with -pct." << endl << endl;
+        
     cerr << "\t-s\t"                << "Define -l and -r based on strand." << endl;
     cerr                            << "\t\tE.g. if used, -l 500 for a negative-stranded feature, " << endl;
     cerr                            << "\t\tit will add 500 bp downstream.  Default = false." << endl << endl;
 
+    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 << "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;