Author: Michael R. Crusoe
Description: Use the Debian package of fermi-lite

Adjust for the renamed bseq1_t→fml_seq1_t
See https://github.com/lh3/fermi-lite/issues/5

--- vg.orig/Makefile
+++ vg/Makefile
@@ -211,7 +211,6 @@
 GBWTGRAPH_DIR=deps/gbwtgraph
 PROGRESS_BAR_DIR:=deps/progress_bar
 FASTAHACK_DIR:=deps/fastahack
-FERMI_DIR:=deps/fermi-lite
 HTSLIB_DIR:=deps/htslib
 VCFLIB_DIR:=deps/vcflib
 GSSW_DIR:=deps/gssw
@@ -253,7 +252,6 @@
 LIB_DEPS += $(LIB_DIR)/libvcfh.a
 LIB_DEPS += $(LIB_DIR)/libsonlib.a
 LIB_DEPS += $(LIB_DIR)/libpinchesandcacti.a
-LIB_DEPS += $(LIB_DIR)/libfml.a
 LIB_DEPS += $(LIB_DIR)/libsublinearLS.a
 LIB_DEPS += $(LIB_DIR)/libstructures.a
 LIB_DEPS += $(LIB_DIR)/libvw.a
@@ -500,9 +498,6 @@
 $(OBJ_DIR)/sha1.o: $(SHA1_DIR)/sha1.cpp $(SHA1_DIR)/sha1.hpp
 	+$(CXX) $(INCLUDE_FLAGS) $(CXXFLAGS) -c -o $@ $< $(FILTER)
 
-$(LIB_DIR)/libfml.a: $(FERMI_DIR)/*.h $(FERMI_DIR)/*.c
-	. ./source_me.sh && cd $(FERMI_DIR) && $(MAKE) $(FILTER) && cp *.h $(CWD)/$(INC_DIR)/ && cp libfml.a $(CWD)/$(LIB_DIR)/
-
 # We don't need to hack the build to point at our htslib because sublinearLS gets its htslib from the include flags we set
 $(LIB_DIR)/libsublinearLS.a: $(LINLS_DIR)/src/*.cpp $(LINLS_DIR)/src/*.hpp $(LIB_DIR)/libhts.a
 	. ./source_me.sh && cd $(LINLS_DIR) && $(MAKE) clean && INCLUDE_FLAGS="-I$(CWD)/$(INC_DIR)" $(MAKE) libs $(FILTER) && cp lib/libsublinearLS.a $(CWD)/$(LIB_DIR)/ && mkdir -p $(CWD)/$(INC_DIR)/sublinearLS && cp src/*.hpp $(CWD)/$(INC_DIR)/sublinearLS/
--- vg.orig/src/srpe.cpp
+++ vg/src/srpe.cpp
@@ -70,7 +70,7 @@
 
     }
 
-    void SRPE::aln_to_bseq(Alignment& a, bseq1_t* read){
+    void SRPE::aln_to_bseq(Alignment& a, fml_seq1_t* read){
         read->seq = (char*) a.sequence().c_str();
         read->qual = (char*) a.quality().c_str();
         read->l_seq = a.sequence().length();
@@ -95,7 +95,7 @@
     void SRPE::assemble(vector<Alignment> alns, vector<fml_utg_t>& unitigs){
         int n_seqs, n_utgs;
         n_seqs = alns.size();
-        bseq1_t* mr_bseqs = new bseq1_t [alns.size()];
+        fml_seq1_t* mr_bseqs = new fml_seq1_t [alns.size()];
         for (int i = 0; i < n_seqs; ++i){
             aln_to_bseq( alns[i], mr_bseqs + i );
         }
--- vg.orig/src/srpe.hpp
+++ vg/src/srpe.hpp
@@ -155,7 +155,7 @@
             double discordance_score(vector<Alignment> alns, VG* subgraph);
 
             // Convert Alignments to the read-like objects Fermi-lite uses in assembly
-            void aln_to_bseq(Alignment& a, bseq1_t* read);
+            void aln_to_bseq(Alignment& a, fml_seq1_t* read);
 
             // Assemble a set of alignments into a set of unitigs
             // UNITIGS ARE GRAPH ELEMENTS - you could make them subgraphs.
