nucBed now obeys strand'

src/nucBed/nucBed.cpp

@@ -13,13 +13,15 @@
 #include "nucBed.h"
 
 
-NucBed::NucBed(string &dbFile, string &bedFile, bool printSeq, bool hasPattern, const string &pattern) {
+NucBed::NucBed(string &dbFile, string &bedFile, bool printSeq, 
+               bool hasPattern, const string &pattern, bool forceStrand) {
 
     _dbFile       = dbFile;
     _bedFile      = bedFile;
     _printSeq     = printSeq;
     _hasPattern   = hasPattern;
     _pattern      = pattern;
+    _forceStrand  = forceStrand;
     
     _bed = new BedFile(_bedFile);
 
@@ -129,7 +131,10 @@ void NucBed::ProfileDNA() {
                     // grab the dna at this interval
                     int length = bed.end - bed.start;
                     // report the sequence's content
-                    ReportDnaProfile(bed, fr.getSubSequence(bed.chrom, bed.start, length), length);
+                    string dna = fr.getSubSequence(bed.chrom, bed.start, length);
+                    if ((_forceStrand == true) && (bed.strand == "-"))
+                        reverseComplement(dna);
+                    ReportDnaProfile(bed, dna, length);
                     bed = nullBed;
                 }
                 else

src/nucBed/nucBed.h

@@ -29,7 +29,9 @@ class NucBed {
 public:
 
     // constructor
-    NucBed(string &dbFile, string &bedFile, bool printSeq, bool hasPattern, const string &pattern);
+    NucBed(string &dbFile, string &bedFile, bool printSeq, 
+           bool hasPattern, const string &pattern,
+           bool forceStrand);
     // destructor
     ~NucBed(void);
 
@@ -42,6 +44,7 @@ private:
     bool   _printSeq;
     bool   _hasPattern;
     string _pattern;
+    bool _forceStrand;
 
     // instance of a bed file class.
     BedFile  *_bed;

src/nucBed/nucBedMain.cpp

@@ -39,6 +39,7 @@ int main(int argc, char* argv[]) {
     bool haveBed     = false;
     bool printSeq    = false;
     bool hasPattern  = false;
+    bool forceStrand = false;
 
     // check to see if we should print out some help
     if(argc <= 1) showHelp = true;
@@ -76,6 +77,9 @@ int main(int argc, char* argv[]) {
         else if(PARAMETER_CHECK("-seq", 4, parameterLength)) {
             printSeq = true;
         }
+        else if(PARAMETER_CHECK("-s", 2, parameterLength)) {
+            forceStrand = true;
+        }
         else if(PARAMETER_CHECK("-pattern", 8, parameterLength)) {
             if ((i+1) < argc) {
                 hasPattern = true;
@@ -95,7 +99,7 @@ int main(int argc, char* argv[]) {
 
     if (!showHelp) {
 
-        NucBed *nuc = new NucBed(fastaDbFile, bedFile, printSeq, hasPattern, pattern);
+        NucBed *nuc = new NucBed(fastaDbFile, bedFile, printSeq, hasPattern, pattern, forceStrand);
         delete nuc;
 
         return 0;
@@ -118,6 +122,7 @@ void ShowHelp(void) {
     cerr << "Options: " << endl;
     cerr << "\t-fi\tInput FASTA file" << endl << endl;
     cerr << "\t-bed\tBED/GFF/VCF file of ranges to extract from -fi" << endl << endl;
+    cerr << "\t-s\tProfile the sequence according to strand." << endl << endl;
     cerr << "\t-seq\tPrint the extracted sequence" << endl << endl;
     cerr << "\t-pattern\tReport the number of times a user-defined sequence is observed (case-insensitive)." << endl << endl;