[f-add-tped] fixed genetic map position output

Author: notestaff

configure

@@ -16037,41 +16037,7 @@ else
   :
 fi
 
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether C++ compiler accepts --param max-inline-insns-single=1000 -Wno-unused-function -Wuninitialized -Wredundant-decls -Wpointer-arith -Wcast-qual -Wcast-align -Wformat -Woverloaded-virtual -Wstrict-null-sentinel -Wlogical-op 	-Wmissing-declarations -Winit-self" >&5
-$as_echo_n "checking whether C++ compiler accepts --param max-inline-insns-single=1000 -Wno-unused-function -Wuninitialized -Wredundant-decls -Wpointer-arith -Wcast-qual -Wcast-align -Wformat -Woverloaded-virtual -Wstrict-null-sentinel -Wlogical-op 	-Wmissing-declarations -Winit-self... " >&6; }
-if ${ax_cv_check_cxxflags____param_max_inline_insns_single_1000__Wno_unused_function__Wuninitialized__Wredundant_decls__Wpointer_arith__Wcast_qual__Wcast_align__Wformat__Woverloaded_virtual__Wstrict_null_sentinel__Wlogical_op___Wmissing_declarations__Winit_self+:} false; then :
-  $as_echo_n "(cached) " >&6
-else
-
-  ax_check_save_flags=$CXXFLAGS
-  CXXFLAGS="$CXXFLAGS  --param max-inline-insns-single=1000 -Wno-unused-function -Wuninitialized -Wredundant-decls -Wpointer-arith -Wcast-qual -Wcast-align -Wformat -Woverloaded-virtual -Wstrict-null-sentinel -Wlogical-op 	-Wmissing-declarations -Winit-self"
-  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h.  */
-
-int
-main ()
-{
-
-  ;
-  return 0;
-}
-_ACEOF
-if ac_fn_cxx_try_compile "$LINENO"; then :
-  ax_cv_check_cxxflags____param_max_inline_insns_single_1000__Wno_unused_function__Wuninitialized__Wredundant_decls__Wpointer_arith__Wcast_qual__Wcast_align__Wformat__Woverloaded_virtual__Wstrict_null_sentinel__Wlogical_op___Wmissing_declarations__Winit_self=yes
-else
-  ax_cv_check_cxxflags____param_max_inline_insns_single_1000__Wno_unused_function__Wuninitialized__Wredundant_decls__Wpointer_arith__Wcast_qual__Wcast_align__Wformat__Woverloaded_virtual__Wstrict_null_sentinel__Wlogical_op___Wmissing_declarations__Winit_self=no
-fi
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
-  CXXFLAGS=$ax_check_save_flags
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ax_cv_check_cxxflags____param_max_inline_insns_single_1000__Wno_unused_function__Wuninitialized__Wredundant_decls__Wpointer_arith__Wcast_qual__Wcast_align__Wformat__Woverloaded_virtual__Wstrict_null_sentinel__Wlogical_op___Wmissing_declarations__Winit_self" >&5
-$as_echo "$ax_cv_check_cxxflags____param_max_inline_insns_single_1000__Wno_unused_function__Wuninitialized__Wredundant_decls__Wpointer_arith__Wcast_qual__Wcast_align__Wformat__Woverloaded_virtual__Wstrict_null_sentinel__Wlogical_op___Wmissing_declarations__Winit_self" >&6; }
-if test "x$ax_cv_check_cxxflags____param_max_inline_insns_single_1000__Wno_unused_function__Wuninitialized__Wredundant_decls__Wpointer_arith__Wcast_qual__Wcast_align__Wformat__Woverloaded_virtual__Wstrict_null_sentinel__Wlogical_op___Wmissing_declarations__Winit_self" = xyes; then :
-  WARNFLAGS="${WARNFLAGS} --param max-inline-insns-single=1000 -Wno-unused-function -Wuninitialized -Wredundant-decls -Wpointer-arith -Wcast-qual -Wcast-align -Wformat -Woverloaded-virtual -Wstrict-null-sentinel -Wlogical-op 	-Wmissing-declarations -Winit-self"
-else
-  :
-fi
-
+#AX_CHECK_COMPILE_FLAG([--param max-inline-insns-single=1000 -Wno-unused-function -Wuninitialized -Wredundant-decls -Wpointer-arith -Wcast-qual -Wcast-align -Wformat -Woverloaded-virtual -Wstrict-null-sentinel -Wlogical-op 	-Wmissing-declarations -Winit-self], [WARNFLAGS="${WARNFLAGS} --param max-inline-insns-single=1000 -Wno-unused-function -Wuninitialized -Wredundant-decls -Wpointer-arith -Wcast-qual -Wcast-align -Wformat -Woverloaded-virtual -Wstrict-null-sentinel -Wlogical-op 	-Wmissing-declarations -Winit-self"], [], [])
 
 #
 # LTO (link-time optimization)

configure.ac

@@ -89,7 +89,7 @@ AX_CHECK_COMPILE_FLAG([-Wall], [WARNFLAGS="${WARNFLAGS} -Wall"], [], [])
 AX_CHECK_COMPILE_FLAG([-Wextra], [WARNFLAGS="${WARNFLAGS} -Wextra"], [], [])
 AX_CHECK_COMPILE_FLAG([-Wno-error], [BOOST_CXXFLAGS="${BOOST_CXXFLAGS} -Wno-error"], [], [])
 AX_CHECK_COMPILE_FLAG([-Wdouble-promotion], [WARNFLAGS="${WARNFLAGS} -Wdouble-promotion"], [], [])
-AX_CHECK_COMPILE_FLAG([--param max-inline-insns-single=1000 -Wno-unused-function -Wuninitialized -Wredundant-decls -Wpointer-arith -Wcast-qual -Wcast-align -Wformat -Woverloaded-virtual -Wstrict-null-sentinel -Wlogical-op 	-Wmissing-declarations -Winit-self], [WARNFLAGS="${WARNFLAGS} --param max-inline-insns-single=1000 -Wno-unused-function -Wuninitialized -Wredundant-decls -Wpointer-arith -Wcast-qual -Wcast-align -Wformat -Woverloaded-virtual -Wstrict-null-sentinel -Wlogical-op 	-Wmissing-declarations -Winit-self"], [], [])
+#AX_CHECK_COMPILE_FLAG([--param max-inline-insns-single=1000 -Wno-unused-function -Wuninitialized -Wredundant-decls -Wpointer-arith -Wcast-qual -Wcast-align -Wformat -Woverloaded-virtual -Wstrict-null-sentinel -Wlogical-op 	-Wmissing-declarations -Winit-self], [WARNFLAGS="${WARNFLAGS} --param max-inline-insns-single=1000 -Wno-unused-function -Wuninitialized -Wredundant-decls -Wpointer-arith -Wcast-qual -Wcast-align -Wformat -Woverloaded-virtual -Wstrict-null-sentinel -Wlogical-op 	-Wmissing-declarations -Winit-self"], [], [])
 
 #
 # LTO (link-time optimization)

cosi/cositop.cc

@@ -326,7 +326,7 @@ CoSiMain::cosi_main(int argc, char *argv[]) {
 		if ( freqsOnly ) cosi.getMutate()->writeTreeSize();
 		if ( msOutput || !tpedOutputPfx.empty() || !outfilebase.empty() || cosi.getCondSnpMgr() || customStats ) {
 			//PRINT( "freezing" );
-			muts->freeze( params->getInfSites() || msOutput || !tpedOutputPfx.empty() || cosi.getCondSnpMgr(),
+			muts->freeze( params->getInfSites() || msOutput || cosi.getCondSnpMgr(),
 										cosi.getGenMap()->recomb_get_length() );
 			//PRINT( "frozen" );
 

cosi/mutlist.cc

@@ -434,7 +434,8 @@ void Mutlist::print_haps_ms( std::ostream& strm,
 		// }
 		// //PRINT( "wrote header" );
 
-
+		len_bp_t region_len_bp = genMap->recomb_get_length();
+		glen_cM_t region_len_cM = genMap->getRegionRecombRateAbs() * 100.0 ;
 
 		unsigned snpId=0;
 		std::vector< leaf_id_t > leavesVec;
@@ -447,8 +448,8 @@ void Mutlist::print_haps_ms( std::ostream& strm,
 
 			const char *line_pop = line.get();
 			for ( size_t pop_idx = 0; pop_idx < leavesInfo->popNames.size(); ++pop_idx ) {
-				outfs[pop_idx] << "1 " << snpId << " " << genMap->norm2orig_gd(genMap->getGdPos( m->loc )) << " " << 
-					int(genMap->norm2orig_pd(get_ploc( m->loc ))) << " ";
+				outfs[pop_idx] << "1 " << snpId << " " << (region_len_cM * ToDouble(genMap->getGdPos( m->loc ))) << " " << 
+					int(region_len_bp * ToDouble(get_ploc( m->loc ))) << " ";
 				size_t line_pop_sz = 2 * leavesInfo->sampleSizes[ pop_idx ];
 				std::string line_pop_str( line_pop, line_pop_sz );
 				outfs[pop_idx] << line_pop_str << "\n";