Michael R. Crusoe · Michael R. Crusoe · Michael R. Crusoe · Michael R. Crusoe · Michael R. Crusoe · Michael R. Crusoe
--- a/debian/changelog
+++ b/debian/changelog
@@ -2,4 +2,4 @@ vg (1.21.0+ds-1) UNRELEASED; urgency=medium

  * Initial release. (Closes: #939537)

- -- Michael R. Crusoe <michael.crusoe@gmail.com>  Sun, 12 Jan 2020 08:30:00 +0100
+ -- Michael R. Crusoe <michael.crusoe@gmail.com>  Mon, 13 Jan 2020 11:32:02 +0100
--- a/debian/control
+++ b/debian/control
@@ -55,7 +55,8 @@ Build-Depends: debhelper-compat (= 12),
               fastahack,
               libsmithwaterman-dev,
               libjs-d3,
-               libdivsufsort-dev
+               libdivsufsort-dev,
+               libtsl-hopscotch-map-dev
 #              libvcflib-dev (>= 1.0),
 #              libhts-dev
 #              libsdsl-dev,

--- a/debian/patches/hardening_flags
+++ b/debian/patches/hardening_flags
--- a/debian/patches/no_need_for_snappy
+++ b/debian/patches/no_need_for_snappy
 Author: Michael R. Crusoe <michael.crusoe@gmail.com>
 Description: Due to other patches, snappy is no longer a dependency
--- a/Makefile
-+++ b/Makefile
-@@ -206,7 +206,6 @@ CONFIGURATION_OBJ =
+--- vg.orig/Makefile
+++ vg/Makefile
+@@ -206,7 +206,6 @@
 
 LOCKFREE_MALLOC_DIR:=deps/lockfree-malloc
 SDSL_DIR:=deps/sdsl-lite
@@ -10,7 +10,7 @@ Description: Due to other patches, snappy is no longer a dependency
 GCSA2_DIR:=deps/gcsa2
 GBWT_DIR:=deps/gbwt
 GBWTGRAPH_DIR=deps/gbwtgraph
-@@ -248,7 +247,6 @@ DEP_OBJ += $(OBJ_DIR)/Fasta.o
+@@ -248,7 +247,6 @@
 LIB_DEPS =
 LIB_DEPS += $(LIB_DIR)/libsdsl.a
 LIB_DEPS += $(LIB_DIR)/libssw.a
@@ -18,7 +18,7 @@ Description: Due to other patches, snappy is no longer a dependency
 LIB_DEPS += $(LIB_DIR)/libgcsa2.a
 LIB_DEPS += $(LIB_DIR)/libgbwt.a
 LIB_DEPS += $(LIB_DIR)/libgbwtgraph.a
-@@ -366,11 +364,6 @@ endif
+@@ -366,11 +364,6 @@
 $(LIB_DIR)/libssw.a: $(SSW_DIR)/*.c $(SSW_DIR)/*.h
 	+. ./source_me.sh && cd $(SSW_DIR) && $(MAKE) $(FILTER) && ar rs $(CWD)/$(LIB_DIR)/libssw.a ssw.o ssw_cpp.o && cp ssw_cpp.h ssw.h $(CWD)/$(LIB_DIR)
 

--- a/debian/patches/no_pg
+++ b/debian/patches/no_pg
 Author: Michael R. Crusoe <michael.crusoe@gmail.com>
 Description: Ensure that we don't accidentally include profile mode
--- a/deps/gfakluge/makefile.detuned
-+++ b/deps/gfakluge/makefile.detuned
+--- vg.orig/deps/gfakluge/makefile.detuned
+++ vg/deps/gfakluge/makefile.detuned
 @@ -1,5 +1,5 @@
 CXX?=g++
 -CXXFLAGS:=-O0 -pipe -std=c++11 -pg -ggdb
@@ -9,9 +9,9 @@ Description: Ensure that we don't accidentally include profile mode
 
 
 BIN_DIR:=bin
--- a/deps/sonLib/include.mk
-+++ b/deps/sonLib/include.mk
-@@ -54,7 +54,7 @@ cflags_ultraDbg = -Wall -Werror --pedant
+--- vg.orig/deps/sonLib/include.mk
+++ vg/deps/sonLib/include.mk
+@@ -54,7 +54,7 @@
 cppflags_ultraDbg = -g -O1 -fno-inline -fno-omit-frame-pointer -fsanitize=address
 
 #Profile flags
@@ -20,9 +20,9 @@ Description: Ensure that we don't accidentally include profile mode
 
 #Flags to use
 ifndef CGL_DEBUG
--- a/deps/vcflib/Makefile
-+++ b/deps/vcflib/Makefile
-@@ -158,7 +158,7 @@ profiling:
+--- vg.orig/deps/vcflib/Makefile
+++ vg/deps/vcflib/Makefile
+@@ -158,7 +158,7 @@
 	$(MAKE) CXXFLAGS="$(CXXFLAGS) -g" all
 
 gprof:
@@ -31,9 +31,9 @@ Description: Ensure that we don't accidentally include profile mode
 
 $(OBJECTS): $(SOURCES) $(HEADERS) $(TABIX) multichoose pre $(SMITHWATERMAN) $(FILEVERCMP) $(FASTAHACK)
 	$(CXX) -c -o $@ src/$(*F).cpp $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) && cp src/*.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
--- a/deps/vowpal_wabbit/Makefile
-+++ b/deps/vowpal_wabbit/Makefile
-@@ -103,7 +103,7 @@ vw:
+--- vg.orig/deps/vowpal_wabbit/Makefile
+++ vg/deps/vowpal_wabbit/Makefile
+@@ -103,7 +103,7 @@
 	cd vowpalwabbit; $(MAKE) -j $(NPROCS) things
 
 #Target-specific flags for a profiling build.  (Copied from line 70)
@@ -42,7 +42,7 @@ Description: Ensure that we don't accidentally include profile mode
 vw_gcov: CXX = g++
 vw_gcov:
 	cd vowpalwabbit && env LDFLAGS="-fprofile-arcs -ftest-coverage -lgcov"; $(MAKE) -j $(NPROCS) things
-@@ -115,7 +115,7 @@ library_example: vw
+@@ -115,7 +115,7 @@
 	cd library; $(MAKE) -j $(NPROCS) things
 
 #Target-specific flags for a profiling build.  (Copied from line 70)

--- a/debian/patches/no_rpath
+++ b/debian/patches/no_rpath
 Author: Michael R. Crusoe <michael.crusoe@gmail.com>
 Description: don't use rpath
--- a/Makefile
-+++ b/Makefile
-@@ -128,8 +128,6 @@ ifeq ($(shell uname -s),Darwin)
+--- vg.orig/Makefile
+++ vg/Makefile
+@@ -128,8 +128,6 @@
 
 else
     # We are not running on OS X

--- a/debian/patches/parallize_better
+++ b/debian/patches/parallize_better
 From: Michael R. Crusoe <michael.crusoe@gmail.com>
-Subject: improve build parallization
+Subject: improve build parallelization
 --- vg.orig/deps/sonLib/externalTools/Makefile
 +++ vg/deps/sonLib/externalTools/Makefile
 @@ -8,13 +8,13 @@

--- a/debian/patches/series
+++ b/debian/patches/series
@@ -18,8 +18,10 @@ use_packaged_fastahack
 #use_packaged_htslib  # waiting on https://github.com/samtools/htslib/pull/904/files or similiar to be merged & new htslib release
 #use_packaged_vw # debian package is out of date, missing array_parameters.h, and not in testing/stable
 #use_packaged_sdsl # fails many tests, local copy is a newer snapshot than Debian's
+#use_packaged_protobuf ?
 hardening_flags
 use_packaged_smithwaterman
 static
 use_packaged_lz4
 parallize_better
+use_packaged_libtsl-hopscotch-map-dev
--- a/debian/patches/spelling
+++ b/debian/patches/spelling
 From: Michael R. Crusoe <michael.crusoe@gmail.com>
 Subject: fix spelling typos
--- a/src/unittest/genotypekit.cpp
-+++ b/src/unittest/genotypekit.cpp
-@@ -431,7 +431,7 @@ TEST_CASE("ExhaustiveTraversalFinder fin
+--- vg.orig/src/unittest/genotypekit.cpp
+++ vg/src/unittest/genotypekit.cpp
+@@ -431,7 +431,7 @@
   REQUIRE(found_trav_2);
 }
 
@@ -11,9 +11,9 @@ Subject: fix spelling typos
 
   SECTION("Directed cycle does not count as ultrabubble") {
     
--- a/src/unittest/aligner.cpp
-+++ b/src/unittest/aligner.cpp
-@@ -123,7 +123,7 @@ TEST_CASE("Full-length bonus can hold do
+--- vg.orig/src/unittest/aligner.cpp
+++ vg/src/unittest/aligner.cpp
+@@ -123,7 +123,7 @@
     aligner_1.align(aln1, graph, true, false);
     aligner_2.align(aln2, graph, true, false);
     
@@ -22,7 +22,7 @@ Subject: fix spelling typos
         REQUIRE(aln1.path().mapping_size() == 1);
         REQUIRE(aln1.path().mapping(0).position().node_id() == n0->id());
         REQUIRE(aln1.path().mapping(0).position().offset() == 2);
-@@ -158,7 +158,7 @@ TEST_CASE("Full-length bonus can hold do
+@@ -158,7 +158,7 @@
     aligner_1.align(aln1, graph, true, false);
     aligner_2.align(aln2, graph, true, false);
     
@@ -31,9 +31,9 @@ Subject: fix spelling typos
         REQUIRE(aln1.path().mapping_size() == 1);
         REQUIRE(aln1.path().mapping(0).position().node_id() == n0->id());
         REQUIRE(aln1.path().mapping(0).position().offset() == 0);
--- a/src/subcommand/mod_main.cpp
-+++ b/src/subcommand/mod_main.cpp
-@@ -45,7 +45,7 @@ void help_mod(char** argv) {
+--- vg.orig/src/subcommand/mod_main.cpp
+++ vg/src/subcommand/mod_main.cpp
+@@ -45,7 +45,7 @@
          << "                            edges from old to new copies to convert the graph into a DAG" << endl
          << "                            until the shortest path through each SCC is N bases long" << endl
          << "    -L, --dagify-len-max N  stop a dagification step if the unrolling component has this much sequence" << endl
@@ -42,9 +42,9 @@ Subject: fix spelling typos
          << "                            component of the graph" << endl
          << "    -O, --orient-forward    orient the nodes in the graph forward" << endl
          << "    -N, --remove-non-path   keep only nodes and edges which are part of paths" << endl
--- a/src/subcommand/find_main.cpp
-+++ b/src/subcommand/find_main.cpp
-@@ -50,7 +50,7 @@ void help_find(char** argv) {
+--- vg.orig/src/subcommand/find_main.cpp
+++ vg/src/subcommand/find_main.cpp
+@@ -50,7 +50,7 @@
          << "sequences:" << endl
          << "    -g, --gcsa FILE        use this GCSA2 index of the sequence space of the graph" << endl
          << "    -z, --kmer-size N      split up --sequence into kmers of size N" << endl
@@ -53,9 +53,9 @@ Subject: fix spelling typos
          << "    -S, --sequence STR     search for sequence STR using --kmer-size kmers" << endl
          << "    -M, --mems STR         describe the super-maximal exact matches of the STR (gcsa2) in JSON" << endl
          << "    -B, --reseed-length N  find non-super-maximal MEMs inside SMEMs of length at least N" << endl
--- a/src/subcommand/genotype_main.cpp
-+++ b/src/subcommand/genotype_main.cpp
-@@ -34,7 +34,7 @@ void help_genotype(char** argv) {
+--- vg.orig/src/subcommand/genotype_main.cpp
+++ vg/src/subcommand/genotype_main.cpp
+@@ -34,7 +34,7 @@
          << "    -A, --no_indel_realign  disable indel realignment" << endl
          << "    -d, --het_prior_denom   denominator for prior probability of heterozygousness" << endl
          << "    -P, --min_per_strand    min unique reads per strand for a called allele to accept a call" << endl
@@ -64,9 +64,9 @@ Subject: fix spelling typos
          << "    -T, --traversal         traversal finder to use {reads, exhaustive, representative, adaptive} (adaptive)" << endl
          << "    -p, --progress          show progress" << endl
          << "    -t, --threads N         number of threads to use" << endl;
--- a/src/subcommand/gamcompare_main.cpp
-+++ b/src/subcommand/gamcompare_main.cpp
-@@ -23,7 +23,7 @@ void help_gamcompare(char** argv) {
+--- vg.orig/src/subcommand/gamcompare_main.cpp
+++ vg/src/subcommand/gamcompare_main.cpp
+@@ -23,7 +23,7 @@
          << endl
          << "options:" << endl
          << "    -r, --range N            distance within which to consider reads correct" << endl
@@ -75,9 +75,9 @@ Subject: fix spelling typos
          << "    -a, --aligner            aligner name for TSV output [\"vg\"]" << endl
          << "    -t, --threads N          number of threads to use" << endl;
 }
--- a/src/subcommand/view_main.cpp
-+++ b/src/subcommand/view_main.cpp
-@@ -73,7 +73,7 @@ void help_view(char** argv) {
+--- vg.orig/src/subcommand/view_main.cpp
+++ vg/src/subcommand/view_main.cpp
+@@ -73,7 +73,7 @@
          << "    -X, --fastq-out            output fastq (input defaults to GAM)" << endl
          << "    -i, --interleaved          fastq is interleaved paired-ended" << endl
 
@@ -86,9 +86,9 @@ Subject: fix spelling typos
          << "    -l, --pileup-in            input VG Pileup format" << endl
 
          << "    -R, --snarl-in             input VG Snarl format" << endl
--- a/src/sampler.cpp
-+++ b/src/sampler.cpp
-@@ -603,7 +603,7 @@ NGSSimulator::NGSSimulator(PathPositionH
+--- vg.orig/src/sampler.cpp
+++ vg/src/sampler.cpp
+@@ -603,7 +603,7 @@
         });
     
     if (!source_paths.empty() && !transcript_expressions.empty()) {
@@ -97,9 +97,9 @@ Subject: fix spelling typos
         exit(1);
     }
     
--- a/deps/vowpal_wabbit/vowpalwabbit/parse_args.cc
-+++ b/deps/vowpal_wabbit/vowpalwabbit/parse_args.cc
-@@ -627,7 +627,7 @@ void parse_feature_tweaks(arguments& arg
+--- vg.orig/deps/vowpal_wabbit/vowpalwabbit/parse_args.cc
+++ vg/deps/vowpal_wabbit/vowpalwabbit/parse_args.cc
+@@ -627,7 +627,7 @@
        ||
        interactions_settings_doubled /*settings were restored from model file to file_options and overriden by params from command line*/)
   {
@@ -108,9 +108,9 @@ Subject: fix spelling typos
 
     // in case arrays were already filled in with values from old model file - reset them
     if (!arg.all->pairs.empty()) arg.all->pairs.clear();
--- a/deps/vowpal_wabbit/vowpalwabbit/global_data.h
-+++ b/deps/vowpal_wabbit/vowpalwabbit/global_data.h
-@@ -160,7 +160,7 @@ public:
+--- vg.orig/deps/vowpal_wabbit/vowpalwabbit/global_data.h
+++ vg/deps/vowpal_wabbit/vowpalwabbit/global_data.h
+@@ -160,7 +160,7 @@
       uint64_t hash = uniform_hash((unsigned char*)l.begin, l.end-l.begin, 378401);
       uint64_t id = name2id.get(l, hash);
       if (id != 0) // TODO: memory leak: char* temp
@@ -119,9 +119,9 @@ Subject: fix spelling typos
       size_t len = l.end - l.begin;
       substring l_copy = { calloc_or_throw<char>(len), nullptr };
       memcpy(l_copy.begin, l.begin, len * sizeof(char));
--- a/src/index.cpp
-+++ b/src/index.cpp
-@@ -2140,7 +2140,7 @@ pair<int64_t, int64_t> Index::compare_km
+--- vg.orig/src/index.cpp
+++ vg/src/index.cpp
+@@ -2140,7 +2140,7 @@
             string kmer;
             parse_kmer(key, value, kmer, id, pos);
 
@@ -130,9 +130,9 @@ Subject: fix spelling typos
             if (kmer != prev_kmer) {
 
                 string remk = reverse_complement(kmer);
--- a/deps/vowpal_wabbit/vowpalwabbit/cost_sensitive.cc
-+++ b/deps/vowpal_wabbit/vowpalwabbit/cost_sensitive.cc
-@@ -23,7 +23,7 @@ void name_value(substring &s, v_array<su
+--- vg.orig/deps/vowpal_wabbit/vowpalwabbit/cost_sensitive.cc
+++ vg/deps/vowpal_wabbit/vowpalwabbit/cost_sensitive.cc
+@@ -23,7 +23,7 @@
       THROW("error NaN value for: " << name[0]);
     break;
   default:

--- a/debian/patches/static
+++ b/debian/patches/static
 Author: Michael R. Crusoe <michael.crusoe@gmail.com>
 Description: For Debian, don't statically link to cairo, jansson, libstdc++, libgcc
--- a/Makefile
-+++ b/Makefile
-@@ -36,9 +36,9 @@ INCLUDE_FLAGS:=$(shell pkg-config --cfla
+--- vg.orig/Makefile
+++ vg/Makefile
+@@ -36,9 +36,9 @@
 # Define libraries to link against. Make sure to always link statically against
 # htslib and libdeflate and Protobuf so that we can use position-dependent code
 # there for speed.
-LD_LIB_FLAGS:= -L$(CWD)/$(LIB_DIR) $(CWD)/$(LIB_DIR)/libvgio.a -lvcflib -lgssw -lssw -lprotobuf -lsublinearLS $(CWD)/$(LIB_DIR)/libhts.a -ldeflate -lpthread -ljansson -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -llz4 -lstructures -lvw -lboost_program_options -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph $(shell pkg-config --libs libfastahack) $(shell pkg-config --libs libsmithwaterman)
-+LD_LIB_FLAGS:= -L$(CWD)/$(LIB_DIR) $(CWD)/$(LIB_DIR)/libvgio.a -lz -lvcflib -lgssw -lssw -lprotobuf -lsublinearLS $(CWD)/$(LIB_DIR)/libhts.a -ldeflate -lpthread -ljansson -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -llz4 -lstructures -lvw -lboost_program_options -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph $(shell pkg-config --libs libfastahack) $(shell pkg-config --libs libsmithwaterman)
+-LD_LIB_FLAGS:= -L$(CWD)/$(LIB_DIR) $(CWD)/$(LIB_DIR)/libvgio.a -lvcflib -lgssw -lssw -lprotobuf -lsublinearLS $(CWD)/$(LIB_DIR)/libhts.a -ldeflate -lpthread -ljansson -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lvcfh -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -llz4 -lstructures -lvw -lboost_program_options -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph $(shell pkg-config --libs libfastahack) $(shell pkg-config --libs libsmithwaterman)
+LD_LIB_FLAGS:= -L$(CWD)/$(LIB_DIR) $(CWD)/$(LIB_DIR)/libvgio.a -lz -lvcflib -lgssw -lssw -lprotobuf -lsublinearLS $(CWD)/$(LIB_DIR)/libhts.a -ldeflate -lpthread -ljansson -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lvcfh -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -llz4 -lstructures -lvw -lboost_program_options -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph $(shell pkg-config --libs libfastahack) $(shell pkg-config --libs libsmithwaterman)
 # Use pkg-config to find Cairo and all the libs it uses
 -LD_LIB_FLAGS += $(shell pkg-config --libs --static cairo jansson)
 +LD_LIB_FLAGS += $(shell pkg-config --libs cairo jansson)
 
 # Travis needs -latomic for all builds *but* GCC on Mac
 ifeq ($(strip $(shell $(CXX) -latomic /dev/null -o/dev/null 2>&1 | grep latomic | wc -l)), 0)
-@@ -181,7 +181,7 @@ LD_LIB_FLAGS += -lrocksdb -lbz2
+@@ -181,7 +181,7 @@
 # When building statically, we need to tell the linker not to bail if it sees multiple definitions.
 # libc on e.g. our Jenkins host does not define malloc as weak, so other mallocs can't override it in a static build.
 # TODO: Why did this problem only begin to happen when libvw was added?

--- a/debian/patches/use_packaged_boost
+++ b/debian/patches/use_packaged_boost
 Author: Michael R. Crusoe <michael.crusoe@gmail.com>
 Description: Use the Debian packages of boost-program-options
--- a/Makefile
-+++ b/Makefile
-@@ -231,7 +231,6 @@ STRUCTURES_DIR:=deps/structures
+--- vg.orig/Makefile
+++ vg/Makefile
+@@ -231,7 +231,6 @@
 BACKWARD_CPP_DIR:=deps/backward-cpp
 DOZEU_DIR:=deps/dozeu
 ELFUTILS_DIR:=deps/elfutils
@@ -10,7 +10,7 @@ Description: Use the Debian packages of boost-program-options
 VOWPALWABBIT_DIR:=deps/vowpal_wabbit
 LIBVGIO_DIR:=deps/libvgio
 LIBHANDLEGRAPH_DIR:=deps/libhandlegraph
-@@ -273,7 +272,6 @@ LIB_DEPS += $(LIB_DIR)/libsublinearLS.a
+@@ -273,7 +272,6 @@
 LIB_DEPS += $(LIB_DIR)/libstructures.a
 LIB_DEPS += $(LIB_DIR)/libvw.a
 LIB_DEPS += $(LIB_DIR)/liballreduce.a
@@ -18,7 +18,7 @@ Description: Use the Debian packages of boost-program-options
 LIB_DEPS += $(LIB_DIR)/libvgio.a
 LIB_DEPS += $(LIB_DIR)/libhandlegraph.a
 LIB_DEPS += $(LIB_DIR)/libbdsg.a
-@@ -538,14 +536,14 @@ $(LIB_DIR)/libstructures.a: $(STRUCTURES
+@@ -539,14 +537,14 @@
 # if it doesn't find it, so let it fail.
 # Also, we need to make sure nothing about -fopenmp makes it into the build, in case we are on Clang.
 # vw doesn't need OpenMP
@@ -35,7 +35,7 @@ Description: Use the Debian packages of boost-program-options
 	+. ./source_me.sh && cd $(VOWPALWABBIT_DIR) && CXXFLAGS="$(filter-out -Xpreprocessor -fopenmp,$(CXXFLAGS))" $(MAKE) $(FILTER)
 	+. ./source_me.sh && cd $(VOWPALWABBIT_DIR) && cp vowpalwabbit/.libs/libvw.a vowpalwabbit/.libs/liballreduce.a $(CWD)/$(LIB_DIR)/
 	+. ./source_me.sh && cd $(VOWPALWABBIT_DIR) && mkdir -p $(CWD)/$(INC_DIR)/vowpalwabbit
-@@ -553,17 +551,6 @@ $(LIB_DIR)/libvw.a: $(LIB_DIR)/libboost_
+@@ -554,17 +552,6 @@
 
 $(LIB_DIR)/liballreduce.a: $(LIB_DIR)/libvw.a
 

--- a/debian/patches/use_packaged_elfutils
+++ b/debian/patches/use_packaged_elfutils
 Author: Michael R. Crusoe <michael.crusoe@gmail.com>
 Description: Use the Debian packages for elfutils
--- a/Makefile
-+++ b/Makefile
-@@ -135,7 +135,7 @@ else
+--- vg.orig/Makefile
+++ vg/Makefile
+@@ -135,7 +135,7 @@
     LD_LIB_FLAGS += -rdynamic
 
     # We want to link against the elfutils libraries
@@ -11,7 +11,7 @@ Description: Use the Debian packages for elfutils
 
     # We get OpenMP the normal way, using whatever the compiler knows about
     CXXFLAGS += -fopenmp
-@@ -225,7 +225,6 @@ SSW_DIR:=deps/ssw/src
+@@ -225,7 +225,6 @@
 LINLS_DIR:=deps/sublinear-Li-Stephens
 STRUCTURES_DIR:=deps/structures
 DOZEU_DIR:=deps/dozeu
@@ -19,7 +19,7 @@ Description: Use the Debian packages for elfutils
 VOWPALWABBIT_DIR:=deps/vowpal_wabbit
 LIBVGIO_DIR:=deps/libvgio
 LIBHANDLEGRAPH_DIR:=deps/libhandlegraph
-@@ -270,15 +269,6 @@ LIB_DEPS += $(LIB_DIR)/libvgio.a
+@@ -270,15 +269,6 @@
 LIB_DEPS += $(LIB_DIR)/libhandlegraph.a
 LIB_DEPS += $(LIB_DIR)/libbdsg.a
 LIB_DEPS += $(LIB_DIR)/libxg.a
@@ -35,7 +35,7 @@ Description: Use the Debian packages for elfutils
 
 # common dependencies to build before all vg src files
 DEPS = $(LIB_DEPS)
-@@ -543,10 +533,6 @@ $(INC_DIR)/sha1.hpp: $(SHA1_DIR)/sha1.hp
+@@ -544,27 +534,6 @@
 $(INC_DIR)/dozeu/dozeu.h: $(DOZEU_DIR)/*.h
 	+mkdir -p $(CWD)/$(INC_DIR)/dozeu && cp $(DOZEU_DIR)/*.h $(CWD)/$(INC_DIR)/dozeu/
 
@@ -43,6 +43,23 @@ Description: Use the Debian packages for elfutils
 -
 -$(LIB_DIR)/libdw.a: $(LIB_DIR)/libelf.a
 -
- $(LIB_DIR)/libdwelf.a: $(LIB_DIR)/libelf.a
+-$(LIB_DIR)/libdwelf.a: $(LIB_DIR)/libelf.a
+-
+-$(LIB_DIR)/libdwfl.a: $(LIB_DIR)/libelf.a
+-
+-# We can't build elfutils from Git without "maintainer mode".
+-# There are some release-only headers or something that it complains it can't find otherwise.
+-# We also don't do a normal make and make install here because we don't want to build and install all the elfutils binaries and libasm.
+-$(LIB_DIR)/libelf.a: $(ELFUTILS_DIR)/libebl/*.c $(ELFUTILS_DIR)/libebl/*.h $(ELFUTILS_DIR)/libdw/*.c $(ELFUTILS_DIR)/libdw/*.h $(ELFUTILS_DIR)/libelf/*.c $(ELFUTILS_DIR)/libelf/*.h $(ELFUTILS_DIR)/src/*.c $(ELFUTILS_DIR)/src/*.h
+-	+cd $(CWD)/$(INC_DIR)/ && rm -Rf elfutils gelf.h libelf.h dwarf.h libdwflP.h libdwfl.h libebl.h libelf.h
+-	+. ./source_me.sh && cd $(ELFUTILS_DIR) && autoreconf -i -f && ./configure --enable-maintainer-mode --prefix=$(CWD) $(FILTER)
+-	+. ./source_me.sh && cd $(ELFUTILS_DIR)/libelf && $(MAKE) clean && $(MAKE) libelf.a $(FILTER)
+-	+. ./source_me.sh && cd $(ELFUTILS_DIR)/libebl && $(MAKE) clean && $(MAKE) libebl.a $(FILTER)
+-	+. ./source_me.sh && cd $(ELFUTILS_DIR)/libdwfl && $(MAKE) clean && $(MAKE) libdwfl.a $(FILTER)
+-	+. ./source_me.sh && cd $(ELFUTILS_DIR)/libdwelf && $(MAKE) clean && $(MAKE) libdwelf.a $(FILTER)
+-	+. ./source_me.sh && cd $(ELFUTILS_DIR)/libdw && $(MAKE) clean && $(MAKE) libdw.a known-dwarf.h $(FILTER)
+-	+cd $(ELFUTILS_DIR) && mkdir -p $(CWD)/$(INC_DIR)/elfutils && cp libdw/known-dwarf.h libdw/libdw.h libebl/libebl.h libelf/elf-knowledge.h version.h libdwfl/libdwfl.h libdwelf/libdwelf.h $(CWD)/$(INC_DIR)/elfutils && cp libelf/gelf.h libelf/libelf.h libdw/dwarf.h $(CWD)/$(INC_DIR) && cp libebl/libebl.a libdw/libdw.a libdwfl/libdwfl.a libdwelf/libdwelf.a libelf/libelf.a $(CWD)/$(LIB_DIR)/
+-
+ $(OBJ_DIR)/sha1.o: $(SHA1_DIR)/sha1.cpp $(SHA1_DIR)/sha1.hpp
+ 	+$(CXX) $(INCLUDE_FLAGS) $(CXXFLAGS) -c -o $@ $< $(FILTER)
 
- $(LIB_DIR)/libdwfl.a: $(LIB_DIR)/libelf.a
--- a/debian/patches/use_packaged_fastahack
+++ b/debian/patches/use_packaged_fastahack
 Author: Michael R. Crusoe <michael.crusoe@gmail.com>
 Description: Use the Debian version of fastahack; not working due to vg needing modifications to the upstream sourcecode
--- a/Makefile
-+++ b/Makefile
-@@ -31,12 +31,12 @@ include $(wildcard $(UNITTEST_OBJ_DIR)/*
+--- vg.orig/Makefile
+++ vg/Makefile
+@@ -31,12 +31,12 @@
 CXXFLAGS := -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP $(CXXFLAGS)
 
 # Set include flags. All -I options need to go in here, so the first directory listed is genuinely searched first.
@@ -13,11 +13,11 @@ Description: Use the Debian version of fastahack; not working due to vg needing
 # htslib and libdeflate and Protobuf so that we can use position-dependent code
 # there for speed.
 -LD_LIB_FLAGS:= -L$(CWD)/$(LIB_DIR) $(CWD)/$(LIB_DIR)/libvgio.a -lvcflib -lgssw -lssw -lprotobuf -lsublinearLS $(CWD)/$(LIB_DIR)/libhts.a -ldeflate -lpthread -ljansson -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lvcfh -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -llz4 -lstructures -lvw -lboost_program_options -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph
-+LD_LIB_FLAGS:= -L$(CWD)/$(LIB_DIR) $(CWD)/$(LIB_DIR)/libvgio.a -lvcflib -lgssw -lssw -lprotobuf -lsublinearLS $(CWD)/$(LIB_DIR)/libhts.a -ldeflate -lpthread -ljansson -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -llz4 -lstructures -lvw -lboost_program_options -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph $(shell pkg-config --libs libfastahack)
+LD_LIB_FLAGS:= -L$(CWD)/$(LIB_DIR) $(CWD)/$(LIB_DIR)/libvgio.a -lvcflib -lgssw -lssw -lprotobuf -lsublinearLS $(CWD)/$(LIB_DIR)/libhts.a -ldeflate -lpthread -ljansson -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lvcfh -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -llz4 -lstructures -lvw -lboost_program_options -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph $(shell pkg-config --libs libfastahack)
 # Use pkg-config to find Cairo and all the libs it uses
 LD_LIB_FLAGS += $(shell pkg-config --libs --static cairo jansson)
 
-@@ -208,7 +208,6 @@ GCSA2_DIR:=deps/gcsa2
+@@ -208,7 +208,6 @@
 GBWT_DIR:=deps/gbwt
 GBWTGRAPH_DIR=deps/gbwtgraph
 PROGRESS_BAR_DIR:=deps/progress_bar
@@ -25,7 +25,7 @@ Description: Use the Debian version of fastahack; not working due to vg needing
 HTSLIB_DIR:=deps/htslib
 VCFLIB_DIR:=deps/vcflib
 GSSW_DIR:=deps/gssw
-@@ -232,7 +231,6 @@ BBHASH_DIR=deps/BBHash
+@@ -232,7 +231,6 @@
 DEP_OBJ =
 DEP_OBJ += $(OBJ_DIR)/progress_bar.o
 DEP_OBJ += $(OBJ_DIR)/sha1.o
@@ -33,7 +33,7 @@ Description: Use the Debian version of fastahack; not working due to vg needing
 
 
 # These are libraries that we need to build before we link vg.
-@@ -247,7 +245,6 @@ LIB_DEPS += $(LIB_DIR)/libgbwtgraph.a
+@@ -247,7 +245,6 @@
 LIB_DEPS += $(LIB_DIR)/libhts.a
 LIB_DEPS += $(LIB_DIR)/libvcflib.a
 LIB_DEPS += $(LIB_DIR)/libgssw.a
@@ -41,7 +41,7 @@ Description: Use the Debian version of fastahack; not working due to vg needing
 LIB_DEPS += $(LIB_DIR)/libsonlib.a
 LIB_DEPS += $(LIB_DIR)/libpinchesandcacti.a
 LIB_DEPS += $(LIB_DIR)/libsublinearLS.a
-@@ -320,7 +317,7 @@ get-deps:
+@@ -320,7 +317,7 @@
 # And we have submodule deps to build
 deps: $(DEPS)
 
@@ -50,7 +50,7 @@ Description: Use the Debian version of fastahack; not working due to vg needing
 	. ./source_me.sh && cd test && prove -v t
 
 docs: $(SRC_DIR)/*.cpp $(SRC_DIR)/*.hpp $(SUBCOMMAND_SRC_DIR)/*.cpp $(SUBCOMMAND_SRC_DIR)/*.hpp $(UNITTEST_SRC_DIR)/*.cpp $(UNITTEST_SRC_DIR)/*.hpp
-@@ -389,9 +386,6 @@ $(INC_DIR)/progress_bar.hpp: $(PROGRESS_
+@@ -389,9 +386,6 @@
 $(OBJ_DIR)/progress_bar.o: $(PROGRESS_BAR_DIR)/*.hpp $(PROGRESS_BAR_DIR)/*.cpp
 	+. ./source_me.sh && cd $(PROGRESS_BAR_DIR) && $(MAKE) $(FILTER) && cp progress_bar.o $(CWD)/$(OBJ_DIR)
 
@@ -60,7 +60,7 @@ Description: Use the Debian version of fastahack; not working due to vg needing
 # We have this target to clean up the old Protobuf we used to have.
 # We can remove it after we no longer care about building properly on a dirty
 # build from vg versions that shipped Protobuf themselves.
-@@ -426,9 +420,6 @@ $(LIB_DIR)/libvcflib.a: $(LIB_DIR)/libht
+@@ -427,9 +421,6 @@
 $(VCFLIB_DIR)/bin/vcf2tsv: $(VCFLIB_DIR)/src/*.cpp $(VCFLIB_DIR)/src/*.h $(LIB_DIR)/libvcflib.a
 	+. ./source_me.sh && cd $(VCFLIB_DIR) && HTS_LIB="$(CWD)/$(LIB_DIR)/libhts.a" HTS_INCLUDES="-I$(CWD)/$(INC_DIR)" HTS_LDFLAGS="-L$(CWD)/$(LIB_DIR) $(START_STATIC) -lhts -ldeflate $(END_STATIC) -lpthread -lm -lbz2 -llzma -lz" $(MAKE) vcf2tsv $(FILTER)
 
@@ -70,7 +70,7 @@ Description: Use the Debian version of fastahack; not working due to vg needing
 $(LIB_DIR)/libgssw.a: $(GSSW_DIR)/src/gssw.c $(GSSW_DIR)/src/gssw.h
 	+. ./source_me.sh && cd $(GSSW_DIR) && $(MAKE) $(FILTER) && cp lib/* $(CWD)/$(LIB_DIR)/ && cp obj/* $(CWD)/$(OBJ_DIR) && cp src/*.h $(CWD)/$(INC_DIR)
 
-@@ -447,10 +438,6 @@ $(INC_DIR)/dynamic/dynamic.hpp: $(DYNAMI
+@@ -448,10 +439,6 @@
 $(INC_DIR)/sparsepp/spp.h:
 	+cp -r $(SPARSEPP_DIR)/sparsepp $(INC_DIR)/
 
@@ -81,7 +81,7 @@ Description: Use the Debian version of fastahack; not working due to vg needing
 $(INC_DIR)/gfakluge.hpp: $(DEP_DIR)/gfakluge/src/gfakluge.hpp
 	+cp $(DEP_DIR)/gfakluge/src/*.hpp $(CWD)/$(INC_DIR)/ && cp $(DEP_DIR)/gfakluge/src/tinyFA/*.hpp $(CWD)/$(INC_DIR)/
 
-@@ -659,14 +646,12 @@ clean: clean-vcflib
+@@ -643,14 +630,12 @@
 	$(RM) -r share/
 	cd $(DEP_DIR) && cd sonLib && $(MAKE) clean
 	cd $(DEP_DIR) && cd htslib && $(MAKE) clean
@@ -96,15 +96,15 @@ Description: Use the Debian version of fastahack; not working due to vg needing
 	cd $(DEP_DIR) && cd vcflib && $(MAKE) clean
 	cd $(DEP_DIR) && cd gfakluge && $(MAKE) clean
 	cd $(DEP_DIR) && cd sha1 && $(MAKE) clean
-@@ -686,5 +671,4 @@ clean-rocksdb:
+@@ -664,5 +649,4 @@
 
 clean-vcflib:
 	cd $(DEP_DIR) && cd vcflib && $(MAKE) clean
 -	rm -f $(LIB_DIR)/libvcfh.a
 	cd $(INC_DIR) && rm -f BedReader.h convert.h join.h mt19937ar.h split.h Variant.h vec128int.h veclib_types.h
--- a/test/Makefile
-+++ b/test/Makefile
-@@ -7,15 +7,12 @@ vg:=../bin/vg
+--- vg.orig/test/Makefile
+++ vg/test/Makefile
+@@ -7,15 +7,12 @@
 
 all: test clean
 
@@ -121,9 +121,9 @@ Description: Use the Debian version of fastahack; not working due to vg needing
 $(vg):
 	cd .. && $(MAKE) bin/vg
 
--- a/test/t/02_vg_construct.t
-+++ b/test/t/02_vg_construct.t
-@@ -75,7 +75,7 @@ rm -f fail.vg
+--- vg.orig/test/t/02_vg_construct.t
+++ vg/test/t/02_vg_construct.t
+@@ -75,7 +75,7 @@
 
 # check that we produce a full graph
 
@@ -132,9 +132,9 @@ Description: Use the Debian version of fastahack; not working due to vg needing
 variantbp=$(zcat < small/x.vcf.gz | ../deps/vcflib/bin/vcf2tsv \
     | cut -f 5,4 | tail -n+2 \
     | awk '{ x=length($2)-length($1); if (x > 0) { print x; } else if (x == 0) { print length($2); } }' \
--- a/deps/vcflib/Makefile
-+++ b/deps/vcflib/Makefile
-@@ -119,7 +119,6 @@ BINS = $(addprefix bin/,$(notdir $(BIN_S
+--- vg.orig/deps/vcflib/Makefile
+++ vg/deps/vcflib/Makefile
+@@ -119,7 +119,6 @@
 SHORTBINS = $(notdir $(BIN_SOURCES:.cpp=))
 
 TABIX = tabixpp/tabix.o
@@ -142,7 +142,7 @@ Description: Use the Debian version of fastahack; not working due to vg needing
 SMITHWATERMAN = smithwaterman/SmithWatermanGotoh.o
 REPEATS = smithwaterman/Repeats.o
 INDELALLELE = smithwaterman/IndelAllele.o
-@@ -135,10 +134,8 @@ HTS_INCLUDES ?= -I$(VCF_LIB_LOCAL)/tabix
+@@ -135,10 +134,8 @@
 HTS_LDFLAGS ?= -L$(VCF_LIB_LOCAL)/tabixpp/htslib -lhts -lbz2 -lm -lz -llzma -pthread
 
 
@@ -155,7 +155,7 @@ Description: Use the Debian version of fastahack; not working due to vg needing
 
 all: $(OBJECTS) $(BINS) scriptToBin
 
-@@ -183,9 +180,6 @@ $(LEFTALIGN): $(SMITHWATERMAN)
+@@ -183,9 +180,6 @@
 
 $(INDELALLELE): $(SMITHWATERMAN)
 
@@ -165,7 +165,7 @@ Description: Use the Debian version of fastahack; not working due to vg needing
 #$(FSOM):
 #	cd fsom && $(CXX) $(CXXFLAGS) -c fsom.c -lm
 
-@@ -227,10 +221,8 @@ clean:
+@@ -227,10 +221,8 @@
 	rm -rf $(OBJ_DIR)
 	cd tabixpp && $(MAKE) clean
 	cd smithwaterman && $(MAKE) clean

--- a/debian/patches/use_packaged_fermi-lite
+++ b/debian/patches/use_packaged_fermi-lite
@@ -4,9 +4,9 @@ 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

--- a/Makefile
-+++ b/Makefile
-@@ -211,7 +211,6 @@ GBWT_DIR:=deps/gbwt
+--- vg.orig/Makefile
+++ vg/Makefile
+@@ -211,7 +211,6 @@
 GBWTGRAPH_DIR=deps/gbwtgraph
 PROGRESS_BAR_DIR:=deps/progress_bar
 FASTAHACK_DIR:=deps/fastahack
@@ -14,7 +14,7 @@ See https://github.com/lh3/fermi-lite/issues/5
 HTSLIB_DIR:=deps/htslib
 VCFLIB_DIR:=deps/vcflib
 GSSW_DIR:=deps/gssw
-@@ -253,7 +252,6 @@ LIB_DEPS += $(LIB_DIR)/libgssw.a
+@@ -253,7 +252,6 @@
 LIB_DEPS += $(LIB_DIR)/libvcfh.a
 LIB_DEPS += $(LIB_DIR)/libsonlib.a
 LIB_DEPS += $(LIB_DIR)/libpinchesandcacti.a
@@ -22,7 +22,7 @@ See https://github.com/lh3/fermi-lite/issues/5
 LIB_DEPS += $(LIB_DIR)/libsublinearLS.a
 LIB_DEPS += $(LIB_DIR)/libstructures.a
 LIB_DEPS += $(LIB_DIR)/libvw.a
-@@ -516,9 +514,6 @@ $(LIB_DIR)/libelf.a: $(ELFUTILS_DIR)/lib
+@@ -500,9 +498,6 @@
 $(OBJ_DIR)/sha1.o: $(SHA1_DIR)/sha1.cpp $(SHA1_DIR)/sha1.hpp
 	+$(CXX) $(INCLUDE_FLAGS) $(CXXFLAGS) -c -o $@ $< $(FILTER)
 
@@ -32,9 +32,9 @@ See https://github.com/lh3/fermi-lite/issues/5
 # 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/
--- a/src/srpe.cpp
-+++ b/src/srpe.cpp
-@@ -70,7 +70,7 @@ namespace vg{
+--- vg.orig/src/srpe.cpp
+++ vg/src/srpe.cpp
+@@ -70,7 +70,7 @@
 
     }
 
@@ -43,7 +43,7 @@ See https://github.com/lh3/fermi-lite/issues/5
         read->seq = (char*) a.sequence().c_str();
         read->qual = (char*) a.quality().c_str();
         read->l_seq = a.sequence().length();
-@@ -95,7 +95,7 @@ namespace vg{
+@@ -95,7 +95,7 @@
     void SRPE::assemble(vector<Alignment> alns, vector<fml_utg_t>& unitigs){
         int n_seqs, n_utgs;
         n_seqs = alns.size();
@@ -52,9 +52,9 @@ See https://github.com/lh3/fermi-lite/issues/5
         for (int i = 0; i < n_seqs; ++i){
             aln_to_bseq( alns[i], mr_bseqs + i );
         }
--- a/src/srpe.hpp
-+++ b/src/srpe.hpp
-@@ -155,7 +155,7 @@ public:
+--- 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

--- a/debian/patches/use_packaged_jemalloc
+++ b/debian/patches/use_packaged_jemalloc
 Author: Michael R. Crusoe <michael.crusoe@gmail.com>
 Description: Use the Debian packaged version of jemalloc
--- a/Makefile
-+++ b/Makefile
-@@ -207,7 +207,6 @@ CONFIGURATION_OBJ =
+--- vg.orig/Makefile
+++ vg/Makefile
+@@ -207,7 +207,6 @@
 
 
 RAPTOR_DIR:=deps/raptor
@@ -10,7 +10,7 @@ Description: Use the Debian packaged version of jemalloc
 LOCKFREE_MALLOC_DIR:=deps/lockfree-malloc
 SDSL_DIR:=deps/sdsl-lite
 SNAPPY_DIR:=deps/snappy
-@@ -311,7 +310,6 @@ LINK_DEPS =
+@@ -311,7 +310,6 @@
 
 ifneq ($(shell uname -s),Darwin)
     # Use jemalloc
@@ -18,7 +18,7 @@ Description: Use the Debian packaged version of jemalloc
 	LD_LIB_FLAGS += -ljemalloc
 endif
 
-@@ -374,9 +372,6 @@ endif
+@@ -374,9 +372,6 @@
 test/build_graph: test/build_graph.cpp $(LIB_DIR)/libvg.a $(SRC_DIR)/json2pb.h $(SRC_DIR)/vg.hpp
 	. ./source_me.sh && $(CXX) $(INCLUDE_FLAGS) $(CXXFLAGS) -o test/build_graph test/build_graph.cpp -lvg $(LD_LIB_FLAGS) $(ROCKSDB_LDFLAGS) $(FILTER)
 
@@ -28,3 +28,11 @@ Description: Use the Debian packaged version of jemalloc
 # Use fake patterns to tell Make that this rule generates all these files when run once.
 # Here % should always match "lib" which is a common substring.
 # See https://stackoverflow.com/a/19822767
+@@ -749,7 +744,6 @@
+ 	cd $(DEP_DIR) && cd gfakluge && $(MAKE) clean
+ 	cd $(DEP_DIR) && cd sha1 && $(MAKE) clean
+ 	cd $(DEP_DIR) && cd structures && $(MAKE) clean
+-	cd $(DEP_DIR) && cd jemalloc && $(MAKE) clean || true
+ 	cd $(DEP_DIR) && cd vowpal_wabbit && $(MAKE) clean
+ 	cd $(DEP_DIR) && cd sublinear-Li-Stephens && $(MAKE) clean
+ 	cd $(DEP_DIR) && cd libhandlegraph && $(MAKE) clean
--- a/debian/patches/use_packaged_libbackward-cpp
+++ b/debian/patches/use_packaged_libbackward-cpp
 Author: Michael R. Crusoe <michael.crusoe@gmail.com>
 Description: Use the Debian version of cpp-backward
--- a/Makefile
-+++ b/Makefile
-@@ -227,7 +227,6 @@ DYNAMIC_DIR:=deps/DYNAMIC
+--- vg.orig/Makefile
+++ vg/Makefile
+@@ -227,7 +227,6 @@
 SSW_DIR:=deps/ssw/src
 LINLS_DIR:=deps/sublinear-Li-Stephens
 STRUCTURES_DIR:=deps/structures
@@ -10,7 +10,7 @@ Description: Use the Debian version of cpp-backward
 DOZEU_DIR:=deps/dozeu
 ELFUTILS_DIR:=deps/elfutils
 VOWPALWABBIT_DIR:=deps/vowpal_wabbit
-@@ -297,7 +296,6 @@ DEPS += $(INC_DIR)/sparsepp/spp.h
+@@ -297,7 +296,6 @@
 DEPS += $(INC_DIR)/gfakluge.hpp
 DEPS += $(INC_DIR)/sha1.hpp
 DEPS += $(INC_DIR)/progress_bar.hpp
@@ -18,7 +18,7 @@ Description: Use the Debian version of cpp-backward
 DEPS += $(INC_DIR)/dozeu/dozeu.h
 DEPS += $(INC_DIR)/mmmultimap.hpp
 DEPS += $(INC_DIR)/ips4o.hpp
-@@ -549,9 +547,6 @@ $(LIB_DIR)/liballreduce.a: $(LIB_DIR)/li
+@@ -550,9 +548,6 @@
 $(INC_DIR)/sha1.hpp: $(SHA1_DIR)/sha1.hpp
 	+cp $(SHA1_DIR)/*.h* $(CWD)/$(INC_DIR)/
 

--- a/debian/patches/use_packaged_libdeflate
+++ b/debian/patches/use_packaged_libdeflate
 Author: Michael R. Crusoe <michael.crusoe@gmail.com>
 Description: Use the Debian package for libdeflate
--- a/Makefile
-+++ b/Makefile
-@@ -36,7 +36,7 @@ INCLUDE_FLAGS:=-I$(CWD)/$(INC_DIR) -I. -
+--- vg.orig/Makefile
+++ vg/Makefile
+@@ -36,7 +36,7 @@
 # Define libraries to link against. Make sure to always link statically against
 # htslib and libdeflate and Protobuf so that we can use position-dependent code
 # there for speed.
@@ -11,7 +11,7 @@ Description: Use the Debian package for libdeflate
 # Use pkg-config to find Cairo and all the libs it uses
 LD_LIB_FLAGS += $(shell pkg-config --libs --static cairo jansson)
 
-@@ -233,7 +233,6 @@ DOZEU_DIR:=deps/dozeu
+@@ -233,7 +233,6 @@
 ELFUTILS_DIR:=deps/elfutils
 BOOST_DIR:=deps/boost-subset
 VOWPALWABBIT_DIR:=deps/vowpal_wabbit
@@ -19,7 +19,7 @@ Description: Use the Debian package for libdeflate
 LIBVGIO_DIR:=deps/libvgio
 LIBHANDLEGRAPH_DIR:=deps/libhandlegraph
 LIBBDSG_DIR:=deps/libbdsg
-@@ -275,7 +274,6 @@ LIB_DEPS += $(LIB_DIR)/libstructures.a
+@@ -275,7 +274,6 @@
 LIB_DEPS += $(LIB_DIR)/libvw.a
 LIB_DEPS += $(LIB_DIR)/liballreduce.a
 LIB_DEPS += $(LIB_DIR)/libboost_program_options.a
@@ -27,7 +27,7 @@ Description: Use the Debian package for libdeflate
 LIB_DEPS += $(LIB_DIR)/libvgio.a
 LIB_DEPS += $(LIB_DIR)/libhandlegraph.a
 LIB_DEPS += $(LIB_DIR)/libbdsg.a
-@@ -459,28 +457,11 @@ $(LIB_DIR)/libhandlegraph.a: $(LIBHANDLE
+@@ -459,28 +457,12 @@
 	+. ./source_me.sh && cd $(LIBHANDLEGRAPH_DIR) && cmake . && $(MAKE) $(FILTER) && cp libhandlegraph.a $(CWD)/$(LIB_DIR) && cp -r src/include/handlegraph $(CWD)/$(INC_DIR)
 
 
@@ -47,7 +47,7 @@ Description: Use the Debian package for libdeflate
 -	+. ./source_me.sh && cd $(LIBDEFLATE_DIR) && V=1 $(MAKE) $(FILTER) && cp libdeflate.a $(CWD)/$(LIB_DIR) && cp libdeflate.h $(CWD)/$(INC_DIR)
 -
 -# We build htslib after libdeflate so it can use libdeflate
-# We have to do a full build in order to install, to get the pkg-config file so libvgio can link against it.
+ # We have to do a full build in order to install, to get the pkg-config file so libvgio can link against it.
 # We also have to have the shared libdeflate or we will get complaints that the static one is not position independent.
 # If we need either the library or the pkg-config file (which we didn't used to ship), run the whole build.
 # We use a wildcard match to make sure make understands that both files come from one command run.

--- a/debian/patches/use_packaged_libtsl-hopscotch-map-dev
+++ b/debian/patches/use_packaged_libtsl-hopscotch-map-dev
+From: Michael R. Crusoe <michael.crusoe@gmail.com>
+Subject: Use the tsl-hopscotch-map cmake target
+--- vg.orig/deps/DYNAMIC/CMakeLists.txt
+++ vg/deps/DYNAMIC/CMakeLists.txt
+@@ -14,23 +14,12 @@
+ 
+ include(${CMAKE_ROOT}/Modules/ExternalProject.cmake)
+ 
+-# hopscotch_map
+-ExternalProject_Add(hopscotch_map
+-  GIT_REPOSITORY "https://github.com/Tessil/hopscotch-map.git"
+-  BUILD_IN_SOURCE TRUE
+-  CMAKE_ARGS -DCMAKE_INSTALL_PREFIX:PATH=${INSTALL_DIR} # TODO ADD static build flag
+-  UPDATE_COMMAND ""
+-  INSTALL_COMMAND ""
+-  BUILD_COMMAND ""
+-  CONFIGURE_COMMAND "")
+-ExternalProject_Get_property(hopscotch_map INSTALL_DIR)
+-set(hopscotch_map_INCLUDE "${INSTALL_DIR}/src/hopscotch_map/include/")
+find_package(tsl-hopscotch-map REQUIRED)
+ 
+ include_directories(${PROJECT_SOURCE_DIR}/include)
+ include_directories(${PROJECT_SOURCE_DIR}/include/internal)
+ include_directories(${PROJECT_SOURCE_DIR}/include/algorithms)
+ include_directories(${PROJECT_SOURCE_DIR}/include/algorithms/cw-bwt)
+-include_directories(${INSTALL_DIR}/src/hopscotch_map/include)
+ 
+ message("Building in ${CMAKE_BUILD_TYPE} mode")
+ 
+@@ -54,11 +43,10 @@
+ add_executable(cw-bwt cw-bwt.cpp)
+ add_executable(benchmark benchmark.cpp)
+ 
+-add_dependencies(debug hopscotch_map)
+-add_dependencies(rle_lz77_v1 hopscotch_map)
+-add_dependencies(rle_lz77_v2 hopscotch_map)
+-add_dependencies(h0_lz77 hopscotch_map)
+-add_dependencies(rle_bwt hopscotch_map)
+-add_dependencies(cw-bwt hopscotch_map)
+-add_dependencies(benchmark hopscotch_map)
+-
+target_link_libraries(debug PRIVATE tsl::hopscotch_map)
+target_link_libraries(rle_lz77_v1 PRIVATE tsl::hopscotch_map)
+target_link_libraries(rle_lz77_v2 PRIVATE tsl::hopscotch_map)
+target_link_libraries(h0_lz77 PRIVATE tsl::hopscotch_map)
+target_link_libraries(rle_bwt PRIVATE tsl::hopscotch_map)
+target_link_libraries(cw-bwt PRIVATE tsl::hopscotch_map)
+target_link_libraries(benchmark PRIVATE tsl::hopscotch_map)
+--- vg.orig/Makefile
+++ vg/Makefile
+@@ -431,7 +431,7 @@
+ $(INC_DIR)/dynamic/dynamic.hpp: $(DYNAMIC_DIR)/include/*.hpp $(DYNAMIC_DIR)/include/internal/*.hpp
+ 	rm -Rf $(INC_DIR)/dynamic.hpp $(INC_DIR)/dynamic
+ 	# annoyingly doesn't have an install option on the cmake, so we manually move their external dependency headers
+-	cd $(CWD)/$(DYNAMIC_DIR) && rm -Rf build && mkdir -p build && cd build && cmake .. && make && cp -r hopscotch_map-prefix/src/hopscotch_map/include/* $(CWD)/$(INC_DIR)/
+	cd $(CWD)/$(DYNAMIC_DIR) && rm -Rf build && mkdir -p build && cd build && cmake .. && make 
+ 	# Do the copy of the main file last so we can tell if this recipe failed and redo it.
+ 	# Otherwise we get dynamic.hpp without its deps
+ 	mkdir -p $(INC_DIR)/dynamic && cp -r $(CWD)/$(DYNAMIC_DIR)/include/* $(INC_DIR)/dynamic
--- a/debian/patches/use_packaged_protobuf
+++ b/debian/patches/use_packaged_protobuf
+Author: Michael R. Crusoe <michael.crusoe@gmail.com>
+Description: Use the Debian packaged version of protobuf
+--- vg.orig/Makefile
+++ vg/Makefile
+@@ -35,7 +35,7 @@
+ # Define libraries to link against. Make sure to always link statically against
+ # htslib and libdeflate and Protobuf so that we can use position-dependent code
+ # there for speed.
+-LD_LIB_FLAGS:= -L$(CWD)/$(LIB_DIR) $(CWD)/$(LIB_DIR)/libvgio.a -lhandlegraph -lvcflib -lgssw -lssw $(CWD)/$(LIB_DIR)/libprotobuf.a -lsublinearLS $(CWD)/$(LIB_DIR)/libhts.a -ldeflate -lpthread -ljansson -lncurses -lgcsa2 -lgbwt -ldivsufsort -ldivsufsort64 -lvcfh -lgfakluge -lraptor2 -lsdsl -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -llz4 -lstructures -lvw -lboost_program_options -lallreduce -lbdsg
+LD_LIB_FLAGS:= -L$(CWD)/$(LIB_DIR) $(CWD)/$(LIB_DIR)/libvgio.a -lhandlegraph -lvcflib -lgssw -lssw -lprotobuf -lsublinearLS $(CWD)/$(LIB_DIR)/libhts.a -ldeflate -lpthread -ljansson -lncurses -lgcsa2 -lgbwt -ldivsufsort -ldivsufsort64 -lvcfh -lgfakluge -lraptor2 -lsdsl -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -llz4 -lstructures -lvw -lboost_program_options -lallreduce -lbdsg
+ # Use pkg-config to find Cairo and all the libs it uses
+ LD_LIB_FLAGS += $(shell pkg-config --libs --static cairo jansson)
+ 
+@@ -173,7 +173,6 @@
+ 
+ 
+ RAPTOR_DIR:=deps/raptor
+-PROTOBUF_DIR:=deps/protobuf
+ LOCKFREE_MALLOC_DIR:=deps/lockfree-malloc
+ SDSL_DIR:=deps/sdsl-lite
+ SNAPPY_DIR:=deps/snappy
+@@ -211,7 +210,6 @@
+ # But that requires fancy ar scripting.
+ # If you just pass them to ar it puts the library *file* in libvg where nothing can read it.
+ LIB_DEPS =
+-LIB_DEPS += $(LIB_DIR)/libprotobuf.a
+ LIB_DEPS += $(LIB_DIR)/libsdsl.a
+ LIB_DEPS += $(LIB_DIR)/libssw.a
+ LIB_DEPS += $(LIB_DIR)/libsnappy.a
+@@ -291,13 +289,6 @@
+ 	ln -s `which shuf` $(BIN_DIR)/shuf
+ endif
+ 
+-# Make sure we have protoc built, and the protobuf lib
+-bin/protoc: $(LIB_DIR)/libprotobuf.a
+-$(LIB_DIR)/libprotobuf.a: deps/protobuf/src/google/protobuf/*.cc
+-	rm -rf $(LIB_DIR)/libprotobuf* $(LIB_DIR)/libprotoc*
+-	rm -Rf include/google/protobuf/
+-	+. ./source_me.sh && cd $(PROTOBUF_DIR) && ./autogen.sh && export DIST_LANG=cpp && ./configure --prefix="$(CWD)" $(FILTER) && $(MAKE) $(FILTER) && $(MAKE) install && export PATH=$(CWD)/bin:$$PATH
+-
+ test/build_graph: test/build_graph.cpp $(LIB_DIR)/libvg.a $(SRC_DIR)/json2pb.h $(SRC_DIR)/vg.hpp
+ 	. ./source_me.sh && $(CXX) $(INCLUDE_FLAGS) $(CXXFLAGS) -o test/build_graph test/build_graph.cpp -lvg $(LD_LIB_FLAGS) $(FILTER)
+ 
+@@ -347,7 +338,7 @@
+ # But we don't delete libvgio.dylib; Mac insists on it for some reason.
+ # We also need to clear out the old Protobuf header in case Protobuf updated;
+ # we don't want to accidentally build against it.
+-$(LIB_DIR)/libvgio.a: $(LIB_DIR)/libhts.a $(LIB_DIR)/pkgconfig/htslib.pc $(LIB_DIR)/libprotobuf.a $(LIBVGIO_DIR)/CMakeLists.txt $(LIBVGIO_DIR)/src/*.cpp $(LIBVGIO_DIR)/include/vg/io/*.hpp
+$(LIB_DIR)/libvgio.a: $(LIB_DIR)/libhts.a $(LIB_DIR)/pkgconfig/htslib.pc $(LIBVGIO_DIR)/CMakeLists.txt $(LIBVGIO_DIR)/src/*.cpp $(LIBVGIO_DIR)/include/vg/io/*.hpp
+ 	+rm -f $(CWD)/$(INC_DIR)/vg.pb.h $(CWD)/$(INC_DIR)/vg/vg.pb.h
+ 	+rm -Rf $(CWD)/$(INC_DIR)/vg/io/
+ 	+. ./source_me.sh && cd $(LIBVGIO_DIR) && PKG_CONFIG_PATH=$(CWD)/$(LIB_DIR)/pkgconfig:$(PKG_CONFIG_PATH) cmake -DCMAKE_PREFIX_PATH=$(CWD) -DCMAKE_LIBRARY_PATH=$(CWD)/$(LIB_DIR) -DCMAKE_INSTALL_PREFIX=$(CWD) -DCMAKE_INSTALL_LIBDIR=lib . $(FILTER) && $(MAKE) clean && VERBOSE=1 $(MAKE) $(FILTER) && $(MAKE) install && rm -f $(CWD)/$(LIB_DIR)/libvgio.so
+@@ -579,7 +570,7 @@
+ 	$(RM) -r $(OBJ_DIR)/*.o $(OBJ_DIR)/*.d
+ 	$(RM) -f $(INC_DIR)/vg_git_version.hpp $(INC_DIR)/vg_system_version.hpp
+ 
+-clean: clean-protobuf clean-vcflib
+clean: clean-vcflib
+ 	$(RM) -r $(BIN_DIR)
+ 	$(RM) -r $(LIB_DIR)
+ 	$(RM) -r $(UNITTEST_OBJ_DIR)
+@@ -612,11 +603,6 @@
+ 	# lru_cache is never built because it is header-only.
+ 	# bash-tap is never built either.
+ 
+-clean-protobuf:
+-	cd $(DEP_DIR) && cd protobuf && $(MAKE) clean
+-	rm -f $(LIB_DIR)/libprotobuf.a
+-	rm -rf $(INC_DIR)/google/protobuf/
+-
+ clean-vcflib:
+ 	cd $(DEP_DIR) && cd vcflib && $(MAKE) clean
+ 	rm -f $(LIB_DIR)/libvcfh.a
--- a/debian/patches/use_packaged_raptor2
+++ b/debian/patches/use_packaged_raptor2
 Author: Michael R. Crusoe <michael.crusoe@gmail.com>
 Description: Use the Debian package for raptor/rapper
--- a/Makefile
-+++ b/Makefile
-@@ -204,7 +204,6 @@ CONFIGURATION_OBJ =
+--- vg.orig/Makefile
+++ vg/Makefile
+@@ -204,7 +204,6 @@
 
 
 
@@ -10,7 +10,7 @@ Description: Use the Debian package for raptor/rapper
 LOCKFREE_MALLOC_DIR:=deps/lockfree-malloc
 SDSL_DIR:=deps/sdsl-lite
 SNAPPY_DIR:=deps/snappy
-@@ -259,7 +258,6 @@ LIB_DEPS += $(LIB_DIR)/libgssw.a
+@@ -259,7 +258,6 @@
 LIB_DEPS += $(LIB_DIR)/libvcfh.a
 LIB_DEPS += $(LIB_DIR)/libsonlib.a
 LIB_DEPS += $(LIB_DIR)/libpinchesandcacti.a
@@ -18,7 +18,7 @@ Description: Use the Debian package for raptor/rapper
 LIB_DEPS += $(LIB_DIR)/libfml.a
 LIB_DEPS += $(LIB_DIR)/libsublinearLS.a
 LIB_DEPS += $(LIB_DIR)/libstructures.a
-@@ -285,7 +283,6 @@ DEPS += $(INC_DIR)/progress_bar.hpp
+@@ -285,7 +283,6 @@
 DEPS += $(INC_DIR)/dozeu/dozeu.h
 DEPS += $(INC_DIR)/mmmultimap.hpp
 DEPS += $(INC_DIR)/ips4o.hpp
@@ -26,7 +26,7 @@ Description: Use the Debian package for raptor/rapper
 DEPS += $(INC_DIR)/BooPHF.h
 
 # Only depend on these files for the final linking stage.	
-@@ -333,7 +330,7 @@ get-deps:
+@@ -333,7 +330,7 @@
 # And we have submodule deps to build
 deps: $(DEPS)
 
@@ -35,7 +35,7 @@ Description: Use the Debian package for raptor/rapper
 	. ./source_me.sh && cd test && prove -v t
 
 docs: $(SRC_DIR)/*.cpp $(SRC_DIR)/*.hpp $(SUBCOMMAND_SRC_DIR)/*.cpp $(SUBCOMMAND_SRC_DIR)/*.hpp $(UNITTEST_SRC_DIR)/*.cpp $(UNITTEST_SRC_DIR)/*.hpp
-@@ -484,23 +481,6 @@ $(LIB_DIR)/libsonlib.a: $(CWD)/$(DEP_DIR
+@@ -485,23 +482,6 @@
 $(LIB_DIR)/libpinchesandcacti.a: $(LIB_DIR)/libsonlib.a $(CWD)/$(DEP_DIR)/pinchesAndCacti/inc/*.h $(CWD)/$(DEP_DIR)/pinchesAndCacti/impl/*.c
 	+. ./source_me.sh && cd $(DEP_DIR)/pinchesAndCacti && $(MAKE) $(FILTER) && cd $(CWD)/$(DEP_DIR)/sonLib && cp lib/stPinchesAndCacti.a $(CWD)/$(LIB_DIR)/libpinchesandcacti.a && cp lib/3EdgeConnected.a $(CWD)/$(LIB_DIR)/lib3edgeconnected.a && mkdir -p $(CWD)/$(INC_DIR)/sonLib && cp lib/*.h $(CWD)/$(INC_DIR)/sonLib
 
@@ -59,7 +59,7 @@ Description: Use the Debian package for raptor/rapper
 $(LIB_DIR)/libstructures.a: $(STRUCTURES_DIR)/src/include/structures/*.hpp $(STRUCTURES_DIR)/src/*.cpp $(STRUCTURES_DIR)/Makefile 
 	+. ./source_me.sh && cd $(STRUCTURES_DIR) && $(MAKE) clean && $(MAKE) lib/libstructures.a $(FILTER) && cp lib/libstructures.a $(CWD)/$(LIB_DIR)/ && cp -r src/include/structures $(CWD)/$(INC_DIR)/
 
-@@ -722,7 +702,6 @@ clean: clean-vcflib
+@@ -705,7 +685,6 @@
 	cd $(DEP_DIR) && cd sublinear-Li-Stephens && $(MAKE) clean
 	cd $(DEP_DIR) && cd libhandlegraph && $(MAKE) clean
 	cd $(DEP_DIR) && cd libvgio && $(MAKE) clean