fixing install issues

src/Makefile.am

@@ -5,8 +5,6 @@ CXXFLAGS = -v -g -std=c++11 -Wall -Wextra -Werror
 # this lists the binaries to produce, the (non-PHONY, binary) targets in
 # the previous manual Makefile
 bin_PROGRAMS = ivar
-ivar_SOURCES = ivar.cpp call_consensus_pileup.cpp alignment.cpp suffix_tree.cpp trim_primer_quality.cpp remove_reads_from_amplicon.cpp call_variants.cpp primer_bed.cpp allele_functions.cpp get_masked_amplicons.cpp get_common_variants.cpp parse_gff.cpp ref_seq.cpp interval_tree.cpp saga.cpp gmm.cpp
+ivar_SOURCES = ivar.cpp call_consensus_pileup.cpp alignment.cpp suffix_tree.cpp trim_primer_quality.cpp remove_reads_from_amplicon.cpp call_variants.cpp primer_bed.cpp allele_functions.cpp get_masked_amplicons.cpp get_common_variants.cpp parse_gff.cpp ref_seq.cpp interval_tree.cpp saga.cpp include/armadillo_bits/*.hpp include/armadillo gmm.cpp 
 ivar_LDADD = $(LIBS)
-
-bin_PROGRAMS = armadillo
-armadillo_SOURCES = ./armadillo/*.hpp
+include_HEADERS = include/armadillo_bits/*.hpp

src/gmm.cpp

@@ -1,6 +1,6 @@
-#include <armadillo>
+#include "./include/armadillo"
 
 int gmm_model(){
-  gmm_diag model;
+  //arma::gmm_diag model;
   return(1);
 }