Updated fastaFromBed

src/fastaFromBed/Makefile

@@ -6,12 +6,13 @@ BIN_DIR = ../../bin/
 # define our includes
 # -------------------
 INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
-			-I$(UTILITIES_DIR)/sequenceUtilities/ \
-			-I$(UTILITIES_DIR)/lineFileUtilities/ \
-			-I$(UTILITIES_DIR)/version/ \
-			-I$(UTILITIES_DIR)/gzstream/ \
-			-I$(UTILITIES_DIR)/fileType/ \
-			-I$(UTILITIES_DIR)/Fasta/
+           -I$(UTILITIES_DIR)/version/ \
+           -I$(UTILITIES_DIR)/gzstream/ \
+           -I$(UTILITIES_DIR)/genomeFile/ \
+           -I$(UTILITIES_DIR)/lineFileUtilities/ \
+           -I$(UTILITIES_DIR)/sequenceUtilities/ \
+           -I$(UTILITIES_DIR)/fileType/ \
+           -I$(UTILITIES_DIR)/Fasta/ \
 
 # ----------------------------------
 # define our source and object files
@@ -37,9 +38,9 @@ $(BUILT_OBJECTS): $(SOURCES)
 	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
 
 $(EXT_OBJECTS):
+	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
 	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/sequenceUtilities/
 	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
 	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
 	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/
 	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/Fasta/

src/fastaFromBed/fastaFromBed.cpp

@@ -13,13 +13,10 @@
 #include "fastaFromBed.h"
 
 
-Bed2Fa::Bed2Fa(bool &useName, string &dbFile, string &bedFile,
-    string &fastaOutFile, bool &useFasta, bool &useStrand) {
-
-    if (useName) {
-        _useName = true;
-    }
+Bed2Fa::Bed2Fa(bool useName, const string &dbFile, const string &bedFile,
+    const string &fastaOutFile, bool useFasta, bool useStrand) {
 
+    _useName      = useName;
     _dbFile       = dbFile;
     _bedFile      = bedFile;
     _fastaOutFile = fastaOutFile;
@@ -102,9 +99,9 @@ void Bed2Fa::ExtractDNA() {
     }
 
     // open and memory-map genome file
-    FastaReference fr;
+    FastaReference *fr = new FastaReference;
     bool memmap = true;
-    fr.open(_dbFile, memmap);
+    fr->open(_dbFile, memmap);
 
     BED bed, nullBed;
     int lineNum = 0;
@@ -116,14 +113,13 @@ void Bed2Fa::ExtractDNA() {
         if (bedStatus == BED_VALID) {
             // make sure we are extracting >= 1 bp
             if (bed.zeroLength == false) {
-                size_t seqLength = fr.sequenceLength(bed.chrom);
+                size_t seqLength = fr->sequenceLength(bed.chrom);
                 // make sure this feature will not exceed the end of the chromosome.
                 if ( (bed.start <= seqLength) && (bed.end <= seqLength) ) 
                 {
                     int length = bed.end - bed.start;
-                    sequence = fr.getSubSequence(bed.chrom, bed.start, length);
+                    sequence = fr->getSubSequence(bed.chrom, bed.start, length);
                     ReportDNA(bed, sequence);
-                    bed = nullBed;
                 }
                 else
                 {

src/fastaFromBed/fastaFromBed.h

@@ -29,8 +29,8 @@ class Bed2Fa {
 public:
 
     // constructor
-    Bed2Fa(bool &useName, string &dbFile, string &bedFile, string &fastaOutFile,
-        bool &useFasta, bool &useStrand);
+    Bed2Fa(bool useName, const string &dbFile, const string &bedFile, const string &fastaOutFile,
+        bool useFasta, bool useStrand);
 
     // destructor
     ~Bed2Fa(void);

src/utils/Fasta/Fasta.cpp

@@ -286,7 +286,7 @@ string FastaReference::sequenceNameStartingWith(string seqnameStart) {
     }
 }
 
-string FastaReference::getSubSequence(string seqname, int start, int length) {
+string FastaReference::getSubSequence(const string &seqname, int start, int length) {
     FastaIndexEntry entry = index->entry(seqname);
     if (start < 0 || length < 1) {
         cerr << "Error: cannot construct subsequence with negative offset or length < 1" << endl;
@@ -318,7 +318,7 @@ string FastaReference::getSubSequence(string seqname, int start, int length) {
     return s;
 }
 
-long unsigned int FastaReference::sequenceLength(string seqname) {
+long unsigned int FastaReference::sequenceLength(const string &seqname) {
     FastaIndexEntry entry = index->entry(seqname);
     return entry.length;
 }

src/utils/Fasta/Fasta.h

@@ -70,9 +70,9 @@ class FastaReference {
         string getSequence(string seqname);
         // potentially useful for performance, investigate
         // void getSequence(string seqname, string& sequence);
-        string getSubSequence(string seqname, int start, int length);
+        string getSubSequence(const string &seqname, int start, int length);
         string sequenceNameStartingWith(string seqnameStart);
-        long unsigned int sequenceLength(string seqname);
+        long unsigned int sequenceLength(const string &seqname);
 };
 
 #endif