added seed and version

README.md

@@ -115,7 +115,7 @@ Contact your sequencing center or core and ask them to send you the sequence of
 For single-end, no. For paired-end, mate have to be consecutive in the file (i.e. `First mate 1`, `second mate 1`, `First mate 2`, `second mate 2`, _etc.._ ). This can be done by either using raw data from the sequencer or sorting by name.
 
 ## Does my BAM file have to be unmapped?
-BAM files can also be used to store unmapped reads. Ideally, leehom should be used prior to mapping since reads will map to a more accurate location if the adapters have been removed and overlapping stretches have been merged.
+BAM files can also be used to store unmapped reads. leeHom should be used prior to mapping since reads will map to a more accurate location if the adapters have been removed and overlapping stretches have been merged.
 
 
 ## What do the `FF` tags in the BAM file mean?

src/Makefile

@@ -50,12 +50,22 @@ all:    ${BAMTOOLSLIBOBJ} ${LIBGABLIBOBJ} MergeTrimReads.o leeHom
 %.o: %.cpp
 	${CXX} -c ${CXXFLAGS} $^ 
 
-leeHom: leeHom.o  MergeTrimReads.o ${LIBGABLIBOBJ}
+version.h:
+	./get_version.sh
+
+leeHom: version.h leeHom.o  MergeTrimReads.o ${LIBGABLIBOBJ}
 	@echo "linking"
 	@echo ${LDLIBS}
 	@echo ${LDFLAGS}
 	${CXX} -o $@ $^ $(LDLIBS) $(LDFLAGS) 
 
+static: version.h leeHom.o  MergeTrimReads.o ${LIBGABLIBOBJ}
+	@echo "staic linking"
+	@echo ${LDLIBS}
+	@echo ${LDFLAGS}
+	${CXX} -static -o leeHom $^ $(LDLIBS) $(LDFLAGS) 
+
+
 ${LIBGABINC}/libgab.h:
 	rm -rf ../libgab/
 	mkdir ../libgab/

src/MergeTrimReads.cpp

@@ -411,12 +411,18 @@ void MergeTrimReads::initMerge(){
 inline double MergeTrimReads::randomGen(){
     //    static bool initialized = false;
 
+
     if(initialized == false){
-	struct timeval time;
-	gettimeofday(&time,NULL);
-	srand(time.tv_usec);
+	if(seedSpecified){
+	    srand(seed);
+	}else{
+	    //use time of day as seed
+	    struct timeval time;
+	    gettimeofday(&time,NULL);
+	    srand(time.tv_usec);
+	}
 	initialized=true;
-	return  (double(rand())/double(RAND_MAX));       
+	return  (double(rand())/double(RAND_MAX));	
     }else{
 	return  (double(rand())/double(RAND_MAX));       
     }
@@ -2058,8 +2064,8 @@ MergeTrimReads::MergeTrimReads (const string& forward_, const string& reverse_,
 				const string& key1_, const string& key2_,
 				const bool trimKey_,
 				const string& ikey_, 
-				int trimcutoff_,bool allowMissing_,
-				bool ancientDNA_,double location_,double scale_,bool useDist_,int qualOffset):
+				const int trimcutoff_,const bool allowMissing_,
+				const bool ancientDNA_,const double location_,const double scale_,const bool useDist_,const int qualOffset,const unsigned int seed_,const bool seedSpecified_):
     //bool mergeoverlap_) : 
     min_length (5),
     qualOffset (qualOffset),
@@ -2075,7 +2081,9 @@ MergeTrimReads::MergeTrimReads (const string& forward_, const string& reverse_,
 
     location(location_),
     scale(scale_),
-    useDist(useDist_)
+    useDist(useDist_),
+    seed(seed_),
+    seedSpecified(seedSpecified_)				    
  {
 
      initialized = false;

src/MergeTrimReads.h

@@ -86,6 +86,8 @@ class MergeTrimReads{
 
     size_t min_overlap_seqs;
 
+    unsigned int seed;
+    bool seedSpecified;
 
     /* //  Key variables /// */
     bool handle_key;
@@ -302,7 +304,14 @@ class MergeTrimReads{
  public:
     MergeTrimReads (const string& forward_, const string& reverse_, const string& chimera_,
 		    const string& key1_="", const string& key2_="",const bool trimKey_=false,const string& ikey_="",
-		    int trimcutoff_=1,bool allowMissing_=false,bool ancientDNA_=false,double location_=-1.0,double scale_=-1.0,bool useDist_=false,int    qualOffset=33);
+		    const int trimcutoff_=1,
+		    const bool allowMissing_=false,
+		    const bool ancientDNA_=false,
+		    const double location_=-1.0,
+		    const double scale_=-1.0,
+		    const bool useDist_=false,
+		    const int    qualOffset=33,
+		    const unsigned int seed=0,const bool seedSpecified=false);
 
     MergeTrimReads(const MergeTrimReads & other);
     ~MergeTrimReads();

src/get_version.sh

@@ -0,0 +1,9 @@
+#!/bin/bash
+
+version=$(git describe --tags $(git rev-list --tags --max-count=1))
+
+if [ $? -eq 0 ]; then
+    echo "#define VERSION \"$version\"" > version.h
+else
+    echo "#define VERSION "NA"" > version.h
+fi