Removed temp files, removed hardcoded dependencies to eigen

RAHenriksen · Apr 10, 2024 · c6519c5 · c6519c5
1 parent a2707db
commit c6519c5
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Showing 13 changed files with 16 additions and 30 deletions.
diff --git a/Likelihood.cpp b/Likelihood.cpp
@@ -10,8 +10,8 @@
 #include <zlib.h>
 #include <cmath>
 #include <iomanip>
-#include <eigen3/Eigen/Core>
-#include <eigen3/Eigen/Eigenvalues>
+#include <Eigen/Core>
+#include <Eigen/Eigenvalues>
 #include <ctime>
 #include <getopt.h>
 #include <iostream>
@@ -2658,4 +2658,4 @@ double PMDLik_nb(char reffrag[], char frag[], int L, double lambda, double delta
     }
     //cout<<l_pmd<<"nuc_lliktest\n";
     return l_pmd;
-}
+}
diff --git a/Makefile b/Makefile
@@ -1,7 +1,7 @@
 CC  ?= gcc
 CXX ?= g++
 
-LIBS = -lz -lm -lbz2 -llzma -lpthread -lcurl -lgsl -lgslcblas
+LIBS = -lz -lm -lbz2 -llzma -lpthread -lcurl 
 
 CRYPTO_TRY=$(shell echo 'int main(){}'|$(CXX) -x c++ - -lcrypto 2>/dev/null -o /dev/null; echo $$?)
 ifeq "$(CRYPTO_TRY)" "0"
@@ -85,15 +85,15 @@ PROGRAMS = ngsbriggs
 
 all: $(PROGRAMS) misc
 
-PACKAGE_VERSION  = 0.4
+PACKAGE_VERSION  = 0.01
 
 ifneq "$(wildcard .git)" ""
 PACKAGE_VERSION := $(shell git describe --always --dirty)
 version.h: $(if $(wildcard version.h),$(if $(findstring "$(PACKAGE_VERSION)",$(shell cat version.h)),,force))
 endif
 
 version.h:
-	echo '#define METADAMAGE_VERSION "$(PACKAGE_VERSION)"' > $@
+	echo '#define NGSBRIGS_VERSION "$(PACKAGE_VERSION)"' > $@
 
 .PHONY: all clean install install-all install-misc misc test
 
@@ -130,4 +130,4 @@ install: all
 	$(INSTALL_DIR) $(DESTDIR)$(bindir)
 	$(INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir)
 
-install-all: install install-misc
+install-all: install install-misc
diff --git a/PosteriorProb.cpp b/PosteriorProb.cpp
@@ -11,8 +11,7 @@
 #include <zlib.h>
 #include <cmath>
 #include <iomanip>
-#include <eigen3/Eigen/Core>
-#include <eigen3/Eigen/Eigenvalues>
+
 #include <ctime>
 #include <getopt.h>
 #include <iostream>
@@ -1238,4 +1237,4 @@ bam_hdr_t* CalPostPMDProb(char *refName,char *fname, const char* chromname, cons
     }//STOPHERE
     //free(fname);
     return hdr;
-}
+}
diff --git a/PosteriorProb.h b/PosteriorProb.h
@@ -12,8 +12,7 @@
 #include <zlib.h>
 #include <cmath>
 #include <iomanip>
-#include <eigen3/Eigen/Core>
-#include <eigen3/Eigen/Eigenvalues>
+
 #include <ctime>
 
 double NoPMDGivenAnc_b(char reffrag[], char frag[], int L, double lambda, double delta, double delta_s, double nv);
@@ -26,4 +25,4 @@ double PMDProb(char reffrag[], char frag[], int L, double lambda, double delta,
 
 bam_hdr_t* CalPostPMDProb(char *refName,char *fname, const char* chromname, const char* bedname, char* ofname, char* olik, int mapped_only,int se_only, int mapq, faidx_t *seq_ref, int len_limit, int len_min, char * model, double eps, double lambda, double delta, double delta_s, double nv, double anc_mu, double anc_si, double mod_mu, double mod_si, int isrecal, std::string s);
 
-#endif
+#endif
diff --git a/Recalibration.cpp b/Recalibration.cpp
@@ -9,8 +9,6 @@
 #include <zlib.h>
 #include <cmath>
 #include <iomanip>
-#include <eigen3/Eigen/Core>
-#include <eigen3/Eigen/Eigenvalues>
 #include <ctime>
 #include <getopt.h>
 #include <iostream>
@@ -963,4 +961,4 @@ void *tsk_All_loglike_recalibration_hess_slave(void *dats){
     tsk_struct *ts = (tsk_struct *) &(my_tsk_struct[(size_t) dats]);
     tsk_loglike_recalibration_hess(ts->x,ts->llh_result_hess,ts->reads,ts->from,ts->to,ts->hdr,ts->seq_ref,ts->len_limit, ts->len_min,ts->model,ts->eps,ts->lambda,ts->delta,ts->delta_s,ts->nv);
     pthread_exit(NULL);
-}
+}
diff --git a/Recalibration.h b/Recalibration.h
@@ -12,8 +12,7 @@
 #include <zlib.h>
 #include <cmath>
 #include <iomanip>
-#include <eigen3/Eigen/Core>
-#include <eigen3/Eigen/Eigenvalues>
+
 #include <ctime>
 using namespace std ;
 
@@ -43,4 +42,4 @@ void tsk_loglike_recalibration_hess(const double *x, double **y, std::vector<bam
 
 void *tsk_All_loglike_recalibration_hess_slave(void *dats);
 
-#endif
+#endif
diff --git a/a.out b/a.out
diff --git a/misc.cpp b/misc.cpp
@@ -10,8 +10,6 @@
 #include <zlib.h>
 #include <cmath>
 #include <iomanip>
-#include <eigen3/Eigen/Core>
-#include <eigen3/Eigen/Eigenvalues>
 #include <ctime>
 #include <getopt.h>
 #include <iostream>
@@ -965,4 +963,4 @@ void Calnuclik(char myread[], kstring_t *kstr, char* chromname, uchar chrid, bam
             }
         }
     }
-}
+}
diff --git a/misc.h b/misc.h
@@ -3,8 +3,6 @@
 
 #include <iostream>
 #include <cmath>
-#include <eigen3/Eigen/Core>
-#include <eigen3/Eigen/Eigenvalues>
 #include <string>
 #include <sstream>
 #include <fstream>
@@ -70,4 +68,4 @@ void parse_sequencingdata1(char *refName,char *fname,const char* chromname, cons
 
 void Calnuclik(char myread[], kstring_t *kstr, char* chromname, uchar chrid, bam1_t *b, double PostProb);
 
-#endif
+#endif
diff --git a/ngsBriggs.cpp b/ngsBriggs.cpp
@@ -8,8 +8,6 @@
 #include <zlib.h>
 #include <cmath>
 #include <iomanip>
-#include <eigen3/Eigen/Core>
-#include <eigen3/Eigen/Eigenvalues>
 #include <ctime>
 #include <getopt.h>
 #include <iostream>

diff --git a/ngsBriggs_cli.cpp b/ngsBriggs_cli.cpp
@@ -9,8 +9,6 @@
 #include <zlib.h>
 #include <cmath>
 #include <iomanip>
-#include <eigen3/Eigen/Core>
-#include <eigen3/Eigen/Eigenvalues>
 #include <ctime>
 #include <getopt.h>
 #include <iostream>

diff --git a/ngsbriggs b/ngsbriggs
diff --git a/version.h b/version.h