From 6a6d297b56c40f9a6b77acca0366af977524b268 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Mon, 5 Oct 2020 09:39:20 +0200
Subject: [PATCH 01/34] sync with vgteam's ssw HEAD

---
 deps/ssw | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/deps/ssw b/deps/ssw
index d27667cbb93..f53d459841b 160000
--- a/deps/ssw
+++ b/deps/ssw
@@ -1 +1 @@
-Subproject commit d27667cbb93bab73de3c31bf0a265fd8e8632e72
+Subproject commit f53d459841b632ac6ab0e59e1a0ef6d056034631

From 33b3e33cba52ec88f3a85169ad5602c7ace357ce Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Thu, 25 Jun 2020 16:40:41 +0200
Subject: [PATCH 02/34] enable building on non-x86 systems

---
 .gitmodules       |  5 ++++-
 Makefile          |  5 +++--
 README.md         |  2 +-
 deps/fermi-lite   |  2 +-
 deps/ssw          |  2 +-
 src/crash.cpp     |  2 +-
 src/preflight.cpp | 22 ----------------------
 src/preflight.hpp |  9 +--------
 src/simde         |  1 +
 9 files changed, 13 insertions(+), 37 deletions(-)
 create mode 160000 src/simde

diff --git a/.gitmodules b/.gitmodules
index b746fc44578..49eef9b9080 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -54,7 +54,7 @@
 	url = https://github.com/benedictpaten/sonLib.git
 [submodule "deps/fermi-lite"]
 	path = deps/fermi-lite
-    url = https://github.com/edawson/fermi-lite.git
+	url = https://github.com/mr-c/fermi-lite.git
 [submodule "deps/rocksdb"]
     path = deps/rocksdb
     url = https://github.com/facebook/rocksdb.git
@@ -119,3 +119,6 @@
 [submodule "vgteam_bbhash"]
 	path = deps/BBHash
 	url = https://github.com/vgteam/BBHash.git
+[submodule "src/simde"]
+	path = src/simde
+	url = https://github.com/nemequ/simde-no-tests
diff --git a/Makefile b/Makefile
index eacb40aab6a..1179269d7e0 100644
--- a/Makefile
+++ b/Makefile
@@ -17,7 +17,8 @@ CWD:=$(shell pwd)
 CXX ?= g++
 PKG_CONFIG ?= pkg-config
 
-EXE:=vg
+SFX :=
+EXE:=vg$(SFX)
 
 all: $(BIN_DIR)/$(EXE)
 
@@ -177,7 +178,7 @@ else
     CXXFLAGS += -fopenmp
 
     # We care about building for SSE4.2 only and not AVX, to have vaguely portable binaries
-    CXXFLAGS += -msse4.2
+    # CXXFLAGS += -msse4.2
     
     # Note shared libraries are so files
     SHARED_SUFFIX = so
diff --git a/README.md b/README.md
index 9e6664b2e76..2f09103cbd0 100644
--- a/README.md
+++ b/README.md
@@ -65,7 +65,7 @@ At present, you will need GCC version 4.9 or greater, with support for C++14, to
 
 Other libraries may be required. Please report any build difficulties.
 
-Note that a 64-bit OS is required. Ubuntu 18.04 should work. You will also need a CPU that supports SSE 4.2 to run VG; you can check this with `cat /proc/cpuinfo | grep sse4_2`.
+Note that a 64-bit OS is required. Ubuntu 18.04 should work.
 
 When you are ready, build with `. ./source_me.sh && make`, and run with `./bin/vg`.
 
diff --git a/deps/fermi-lite b/deps/fermi-lite
index cde7871d5a6..e5603862255 160000
--- a/deps/fermi-lite
+++ b/deps/fermi-lite
@@ -1 +1 @@
-Subproject commit cde7871d5a6658be61a7c3995a56ac21fbacf4f4
+Subproject commit e56038622555349707c5cd90c062f0cf3f370b11
diff --git a/deps/ssw b/deps/ssw
index d27667cbb93..f53d459841b 160000
--- a/deps/ssw
+++ b/deps/ssw
@@ -1 +1 @@
-Subproject commit d27667cbb93bab73de3c31bf0a265fd8e8632e72
+Subproject commit f53d459841b632ac6ab0e59e1a0ef6d056034631
diff --git a/src/crash.cpp b/src/crash.cpp
index 2a4f9427b8a..0aefb090bdb 100644
--- a/src/crash.cpp
+++ b/src/crash.cpp
@@ -168,7 +168,7 @@ void emit_stacktrace(int signalNumber, siginfo_t *signalInfo, void *signalContex
         *out << "Caught signal " << signalNumber << " raised at address " << ip << endl;
         // Do our own tracing because backtrace doesn't really work on all platforms.
         stacktrace_manually(*out, signalNumber, ip, bp);
-    #else
+    #elif __x86_64__
         // Linux 64 bit does it this way
         ip = (void*)context->uc_mcontext.gregs[REG_RIP];
         bp = (void**)context->uc_mcontext.gregs[REG_RBP];
diff --git a/src/preflight.cpp b/src/preflight.cpp
index 94c5e6ab8a9..6c97db57103 100644
--- a/src/preflight.cpp
+++ b/src/preflight.cpp
@@ -1,33 +1,11 @@
 #include "preflight.hpp"
 
-#include <iostream>
-#include <cstdlib>
-#include <cpuid.h>
-
 namespace vg {
 
 using namespace std;
 
 void preflight_check() {
     
-    // We assume we are on x86_64 on POSIX (and not Windows).
-    // We use the method of dlib's dlib/simd/simd_check.h
-    
-    // Define a place to put the cpuid info
-    unsigned int cpuid_info[4];
-    
-    // Call cpuid function 1 (which reports SSE4.2, and other stuff up to original AVX)
-    __cpuid(1, cpuid_info[0], cpuid_info[1], cpuid_info[2], cpuid_info[3]);
-    
-    // Bit 20 of result 2 is the SSE 4.2 flag.
-    bool have_sse4_2 = cpuid_info[2] & (1 << 20);
-    
-    if (!have_sse4_2) {
-        cerr << "error[vg::preflight_check]: The CPU does not support SSE4.2 instructions. VG cannot run here. "
-            << "Please use a system with SSE4.2 support." << endl;
-        exit(1);
-    }
-    
 }
 
 }
diff --git a/src/preflight.hpp b/src/preflight.hpp
index b8cb3dda1c5..45a5f495c03 100644
--- a/src/preflight.hpp
+++ b/src/preflight.hpp
@@ -11,14 +11,7 @@
 
 namespace vg {
 
-/// Define a macro to tell things to be built for every architecture, if possible.
-/// This *doesn't* work on Mac with GNU GCC and Apple libc++, because functions
-/// for x86-64 can't use std::endl, so we exclude that combination.
-#if (!defined(__GNUC__) || !defined(_LIBCPP_VERSION) || !defined(__APPLE__))
-    #define VG_PREFLIGHT_EVERYWHERE __attribute__((__target__("arch=x86-64")))
-#else
-    #define VG_PREFLIGHT_EVERYWHERE
-#endif
+#define VG_PREFLIGHT_EVERYWHERE
 
 /// Run a preflight check to make sure that the system is usable for this build of vg.
 /// Aborts with a helpful message if this is not the case.
diff --git a/src/simde b/src/simde
new file mode 160000
index 00000000000..8cd136a43ba
--- /dev/null
+++ b/src/simde
@@ -0,0 +1 @@
+Subproject commit 8cd136a43bae7ab9b82316179b9cef8887726778

From ce555edd43e3aa600262879353f7b4702c03af2d Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Thu, 25 Jun 2020 16:46:30 +0200
Subject: [PATCH 03/34] build arm64

---
 .travis.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 44869200f9a..622ff56e3ed 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -2,7 +2,6 @@
 
 language: cpp
 compiler: gcc
-sudo: required
 dist: bionic
 # We have some shenanigans to let us cache submodules, and update changed files
 # without messing up mtimes and triggering rebuilds unnecessarily. Travis checks
@@ -112,8 +111,6 @@ os:
   - linux
   - osx
 osx_image: xcode12.2
-compiler:
-  - gcc
 env:
   global:
     - DOCS_KEY_ENCRYPTION_LABEL=125272388526
@@ -124,3 +121,5 @@ matrix:
     # We have a special entry to do the docs build
     - os: linux
       env: BUILD_DOCS_ONLY=1
+    - os: linux
+      arch: arm64

From b473df4f163c116d8f30d52ed0f9d08f63b43b31 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Thu, 25 Jun 2020 18:44:45 +0200
Subject: [PATCH 04/34] verbose rocksdb

---
 Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Makefile b/Makefile
index 1179269d7e0..63d2fbfc604 100644
--- a/Makefile
+++ b/Makefile
@@ -438,7 +438,7 @@ $(LIB_DIR)/libsnappy.a: $(SNAPPY_DIR)/*.cc $(SNAPPY_DIR)/*.h
 	+. ./source_me.sh && cd $(SNAPPY_DIR) && ./autogen.sh && CXXFLAGS="$(filter-out -Xpreprocessor -fopenmp,$(CXXFLAGS))" ./configure --prefix=$(CWD) $(FILTER) && CXXFLAGS="$(filter-out -Xpreprocessor -fopenmp,$(CXXFLAGS))" $(MAKE) libsnappy.la $(FILTER) && cp .libs/libsnappy.a $(CWD)/lib/ && cp snappy-c.h snappy-sinksource.h snappy-stubs-public.h snappy.h $(CWD)/include/
 
 $(LIB_DIR)/librocksdb.a: $(LIB_DIR)/libsnappy.a $(ROCKSDB_DIR)/db/*.cc $(ROCKSDB_DIR)/db/*.h
-	+. ./source_me.sh && cd $(ROCKSDB_DIR) && $(ROCKSDB_PORTABLE) DISABLE_JEMALLOC=1 $(MAKE) static_lib $(FILTER) && mv librocksdb.a $(CWD)/${LIB_DIR}/ && cp -r include/* $(CWD)/$(INC_DIR)/
+	+. ./source_me.sh && cd $(ROCKSDB_DIR) && $(ROCKSDB_PORTABLE) DISABLE_JEMALLOC=1 $(MAKE) AM_DEFAULT_VERBOSITY=1 static_lib $(FILTER) && mv librocksdb.a $(CWD)/${LIB_DIR}/ && cp -r include/* $(CWD)/$(INC_DIR)/
 
 $(INC_DIR)/gcsa/gcsa.h: $(LIB_DIR)/libgcsa2.a
 

From d2bb24d6b2447f6e6fa83612456f015dd07d695b Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Sat, 27 Jun 2020 12:27:59 +0200
Subject: [PATCH 05/34] issue with cached deps?

---
 .travis.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 622ff56e3ed..8bdf19fa3b2 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -14,10 +14,10 @@ before_install:
   - if [[ -e deps ]]; then mv deps deps_cached; fi
   - git submodule update --init --recursive
   - rsync -rv --links --checksum deps/ deps_cached/
-  - rm -Rf deps
+  # - rm -Rf deps
   # Keep the cached deps if the right compiler version was used.
   # Otherwise start fresh
-  - if [[ "$TRAVIS_OS_NAME" == "linux" && -e "deps_cached/gcc$(gcc -dumpversion)" ]]; then mv deps_cached deps; fi
+  # - if [[ "$TRAVIS_OS_NAME" == "linux" && -e "deps_cached/gcc$(gcc -dumpversion)" ]]; then mv deps_cached deps; fi
   - if [[ "$TRAVIS_OS_NAME" == "osx" && -e deps_cached/clang ]]; then mv deps_cached deps; fi
   - (ls -lah deps/; ls -lah bin/; ls -lah lib/; ls -lah include/) || true
   - git submodule update --init --recursive

From 10b63f3e7348cbf3dbd73a4fe85610bbc6a41809 Mon Sep 17 00:00:00 2001
From: Adam Novak <anovak@soe.ucsc.edu>
Date: Thu, 28 Jan 2021 00:09:36 +0000
Subject: [PATCH 06/34] Only ask for SSE on x86_64

---
 Makefile | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/Makefile b/Makefile
index 7f3879a1553..c653ba489cb 100644
--- a/Makefile
+++ b/Makefile
@@ -181,9 +181,11 @@ else
     # We get OpenMP the normal way, using whatever the compiler knows about
     CXXFLAGS += -fopenmp
 
-    # We care about building for SSE4.2 only and not AVX, to have vaguely portable binaries
-    CXXFLAGS += -msse4.2
-    
+    ifeq ($(shell arch), x86_64)
+        # We care about building for SSE4.2 only and not AVX, to have vaguely portable binaries
+        CXXFLAGS += -msse4.2
+    endif
+
     # Note shared libraries are so files
     SHARED_SUFFIX = so
     # Define options to start static linking of libraries on GNU ld.

From 6e77c05dc27a6767d2156ca0d4a99e4907165eaa Mon Sep 17 00:00:00 2001
From: Adam Novak <anovak@soe.ucsc.edu>
Date: Thu, 28 Jan 2021 00:21:30 +0000
Subject: [PATCH 07/34] Only lower-bound architecture when on x86

---
 src/preflight.cpp | 3 +++
 src/preflight.hpp | 4 ++--
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/preflight.cpp b/src/preflight.cpp
index 94c5e6ab8a9..8ee3adb352a 100644
--- a/src/preflight.cpp
+++ b/src/preflight.cpp
@@ -10,6 +10,7 @@ using namespace std;
 
 void preflight_check() {
     
+#ifdef __x86_64__
     // We assume we are on x86_64 on POSIX (and not Windows).
     // We use the method of dlib's dlib/simd/simd_check.h
     
@@ -27,6 +28,8 @@ void preflight_check() {
             << "Please use a system with SSE4.2 support." << endl;
         exit(1);
     }
+#endif
+    // If not on x86_64, we are probably on ARM and using fake SSE anyway.
     
 }
 
diff --git a/src/preflight.hpp b/src/preflight.hpp
index b8cb3dda1c5..7db872eab0d 100644
--- a/src/preflight.hpp
+++ b/src/preflight.hpp
@@ -11,10 +11,10 @@
 
 namespace vg {
 
-/// Define a macro to tell things to be built for every architecture, if possible.
+/// Define a macro to tell things to be built for every X86_64 architecture, if possible.
 /// This *doesn't* work on Mac with GNU GCC and Apple libc++, because functions
 /// for x86-64 can't use std::endl, so we exclude that combination.
-#if (!defined(__GNUC__) || !defined(_LIBCPP_VERSION) || !defined(__APPLE__))
+#if defined(__x86_64__) && (!defined(__GNUC__) || !defined(_LIBCPP_VERSION) || !defined(__APPLE__))
     #define VG_PREFLIGHT_EVERYWHERE __attribute__((__target__("arch=x86-64")))
 #else
     #define VG_PREFLIGHT_EVERYWHERE

From e91dd9a09a6f5a0ec43f1d07b27e2a3af2f518da Mon Sep 17 00:00:00 2001
From: Adam Novak <anovak@soe.ucsc.edu>
Date: Wed, 27 Jan 2021 16:56:59 -0800
Subject: [PATCH 08/34] Properly upgrade headers for and call new SSW

---
 Makefile            | 4 ++--
 src/ssw_aligner.cpp | 8 +++++++-
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/Makefile b/Makefile
index 507a7de1901..3c3406c3e00 100644
--- a/Makefile
+++ b/Makefile
@@ -427,8 +427,8 @@ else
 	+. ./source_me.sh && cd $(SDSL_DIR) && BUILD_PORTABLE=1 CXXFLAGS="$(CPPFLAGS) $(CXXFLAGS)" ./install.sh $(CWD) $(FILTER)
 endif
 
-$(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)
+$(LIB_DIR)/libssw.a: $(SSW_DIR)/*.c $(SSW_DIR)/*.cpp $(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 $(CWD)/$(INC_DIR)
 
 # We need to hide -Xpreprocessor -fopenmp from Snappy, at least on Mac, because
 # it will drop the -Xpreprocessor and keep the -fopenmp and upset Clang.
diff --git a/src/ssw_aligner.cpp b/src/ssw_aligner.cpp
index 268eedd040a..64a75277bad 100644
--- a/src/ssw_aligner.cpp
+++ b/src/ssw_aligner.cpp
@@ -23,7 +23,13 @@ Alignment SSWAligner::align(const string& query, const string& ref) {
                                           gap_extension);
     StripedSmithWaterman::Filter filter;
     StripedSmithWaterman::Alignment alignment;
-    aligner.Align(query.c_str(), ref.c_str(), ref.size(), filter, &alignment);
+    
+    // We need to send out own mask length, recommended to be half the sequence length and at least 15.
+    int32_t mask_len = min(max((size_t) 15, query.size()), (size_t) numeric_limits<int32_t>::max());
+    
+    assert(ref.size() <= numeric_limits<int>::max());
+    
+    aligner.Align(query.c_str(), ref.c_str(), (int) ref.size(), filter, &alignment, mask_len);
     return ssw_to_vg(alignment, query, ref);
 }
 

From 77409aecea5c79744d26ceaace7c9ada6c21794c Mon Sep 17 00:00:00 2001
From: Adam Novak <anovak@soe.ucsc.edu>
Date: Thu, 28 Jan 2021 01:01:23 +0000
Subject: [PATCH 09/34] Use vgteam fermi-lite repo

---
 .gitmodules | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitmodules b/.gitmodules
index de3c78d152e..b68d6d05292 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -54,7 +54,7 @@
 	url = https://github.com/benedictpaten/sonLib.git
 [submodule "deps/fermi-lite"]
 	path = deps/fermi-lite
-    url = https://github.com/edawson/fermi-lite.git
+    url = https://github.com/vgteam/fermi-lite.git
 [submodule "deps/gbwt"]
 	path = deps/gbwt
 	url = https://github.com/jltsiren/gbwt.git

From 5a865a9192e35745dae712d933ec7c94e62d8e80 Mon Sep 17 00:00:00 2001
From: Adam Novak <anovak@soe.ucsc.edu>
Date: Thu, 28 Jan 2021 01:01:54 +0000
Subject: [PATCH 10/34] Use non-x86-supporting fermi-lite

---
 deps/fermi-lite | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/deps/fermi-lite b/deps/fermi-lite
index cde7871d5a6..62faee92e49 160000
--- a/deps/fermi-lite
+++ b/deps/fermi-lite
@@ -1 +1 @@
-Subproject commit cde7871d5a6658be61a7c3995a56ac21fbacf4f4
+Subproject commit 62faee92e49f1724a354088cd3fdddfd90829b28

From d1151be6ec75e3848f4fd5e74c94a456c27bc37a Mon Sep 17 00:00:00 2001
From: Adam Novak <anovak@soe.ucsc.edu>
Date: Wed, 27 Jan 2021 17:11:43 -0800
Subject: [PATCH 11/34] Fix preflight includes

---
 src/preflight.cpp | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/src/preflight.cpp b/src/preflight.cpp
index 74b65439edd..fde71e4b8e1 100644
--- a/src/preflight.cpp
+++ b/src/preflight.cpp
@@ -1,5 +1,12 @@
 #include "preflight.hpp"
 
+#include <iostream>
+#include <cstdlib>
+
+#ifdef __x86_64__
+#include <cpuid.h>
+#endif
+
 namespace vg {
 
 using namespace std;

From 58d52437f5f2be780bb92de5d203219ff98639bc Mon Sep 17 00:00:00 2001
From: Adam Novak <anovak@soe.ucsc.edu>
Date: Thu, 28 Jan 2021 10:03:22 -0800
Subject: [PATCH 12/34] Stop overwriting SSW headers with GSSW versions

---
 Makefile  | 2 +-
 deps/gssw | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/Makefile b/Makefile
index 5fe91345485..5e62aa0177e 100644
--- a/Makefile
+++ b/Makefile
@@ -539,7 +539,7 @@ $(FASTAHACK_DIR)/fastahack: $(FASTAHACK_DIR)/*.c $(FASTAHACK_DIR)/*.h $(FASTAHAC
 	+. ./source_me.sh && cd $(FASTAHACK_DIR) && $(MAKE) $(FILTER)
 
 $(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)
+	+. ./source_me.sh && cd $(GSSW_DIR) && $(MAKE) $(FILTER) && cp lib/libgssw.a $(CWD)/$(LIB_DIR)/ && cp src/gssw.h $(CWD)/$(INC_DIR)/
 
 $(INC_DIR)/lru_cache.h: $(DEP_DIR)/lru_cache/*.h $(DEP_DIR)/lru_cache/*.cc
 	+cd $(DEP_DIR)/lru_cache && cp *.h* $(CWD)/$(INC_DIR)/
diff --git a/deps/gssw b/deps/gssw
index 2f219159817..e17bad23ab6 160000
--- a/deps/gssw
+++ b/deps/gssw
@@ -1 +1 @@
-Subproject commit 2f219159817bbe6848feec3f51fbe373742c7abf
+Subproject commit e17bad23ab68cfa9b8668b8298187d0b308b6129

From d8021460468779469be84b23082156518d64a209 Mon Sep 17 00:00:00 2001
From: Adam Novak <anovak@soe.ucsc.edu>
Date: Thu, 28 Jan 2021 10:19:41 -0800
Subject: [PATCH 13/34] Put back dependency cache replacement

---
 .travis.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 8bdf19fa3b2..622ff56e3ed 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -14,10 +14,10 @@ before_install:
   - if [[ -e deps ]]; then mv deps deps_cached; fi
   - git submodule update --init --recursive
   - rsync -rv --links --checksum deps/ deps_cached/
-  # - rm -Rf deps
+  - rm -Rf deps
   # Keep the cached deps if the right compiler version was used.
   # Otherwise start fresh
-  # - if [[ "$TRAVIS_OS_NAME" == "linux" && -e "deps_cached/gcc$(gcc -dumpversion)" ]]; then mv deps_cached deps; fi
+  - if [[ "$TRAVIS_OS_NAME" == "linux" && -e "deps_cached/gcc$(gcc -dumpversion)" ]]; then mv deps_cached deps; fi
   - if [[ "$TRAVIS_OS_NAME" == "osx" && -e deps_cached/clang ]]; then mv deps_cached deps; fi
   - (ls -lah deps/; ls -lah bin/; ls -lah lib/; ls -lah include/) || true
   - git submodule update --init --recursive

From c8e47a23dee6074702521899c192f5dffbdf7126 Mon Sep 17 00:00:00 2001
From: Adam Novak <anovak@soe.ucsc.edu>
Date: Thu, 28 Jan 2021 10:29:27 -0800
Subject: [PATCH 14/34] Try and get out of dependency hell

---
 .travis.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.travis.yml b/.travis.yml
index 622ff56e3ed..a82f54b0d40 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -11,6 +11,10 @@ dist: bionic
 # version back.
 # Doxygen docs depend on Protobuf so we still need to do dep cache stuff for docs.
 before_install:
+  # On ARM Linux, Travis can get backed into a dependency corner trying to
+  # uninstall the libcurl the system came with to obey addons.apt.packages. Try
+  # to get out of it.
+  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo dpkg --configure -a; sudo apt-get install -f; fi
   - if [[ -e deps ]]; then mv deps deps_cached; fi
   - git submodule update --init --recursive
   - rsync -rv --links --checksum deps/ deps_cached/

From 07f45cf0b4325c5f9e614e9e5d4bd44c49de8fce Mon Sep 17 00:00:00 2001
From: Adam Novak <anovak@soe.ucsc.edu>
Date: Mon, 1 Feb 2021 09:18:26 -0800
Subject: [PATCH 15/34] Let make get-deps upgrade packages

---
 Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Makefile b/Makefile
index 5e62aa0177e..3809a1796cd 100644
--- a/Makefile
+++ b/Makefile
@@ -388,7 +388,7 @@ $(LIB_DIR)/libvg.a: $(OBJ) $(ALGORITHMS_OBJ) $(IO_OBJ) $(DEP_OBJ) $(DEPS)
 
 # We have system-level deps to install
 get-deps:
-	sudo apt-get install -qq -y --no-upgrade build-essential git protobuf-compiler libprotoc-dev libjansson-dev libbz2-dev libncurses5-dev automake libtool jq bc rs parallel npm samtools curl unzip redland-utils librdf-dev cmake pkg-config wget gtk-doc-tools raptor2-utils rasqal-utils bison flex gawk libgoogle-perftools-dev liblz4-dev liblzma-dev libcairo2-dev libpixman-1-dev libffi-dev libcairo-dev libprotobuf-dev libboost-all-dev
+	sudo apt-get install -qq -y build-essential git protobuf-compiler libprotoc-dev libjansson-dev libbz2-dev libncurses5-dev automake libtool jq bc rs parallel npm samtools curl unzip redland-utils librdf-dev cmake pkg-config wget gtk-doc-tools raptor2-utils rasqal-utils bison flex gawk libgoogle-perftools-dev liblz4-dev liblzma-dev libcairo2-dev libpixman-1-dev libffi-dev libcairo-dev libprotobuf-dev libboost-all-dev
 
 # And we have submodule deps to build
 deps: $(DEPS)

From 635fcaa6f96bdee9061c6fe841d9b07810aaea2b Mon Sep 17 00:00:00 2001
From: Adam Novak <anovak@soe.ucsc.edu>
Date: Tue, 2 Feb 2021 15:58:08 -0800
Subject: [PATCH 16/34] Make Docker build also run in-container tests

---
 .gitlab-ci.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 6bc04926af3..e051ae26d07 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -86,7 +86,9 @@ build-job:
     - docker login -u "${CI_REGISTRY_USER}" -p "${CI_REGISTRY_PASSWORD}" "${CI_REGISTRY}"
   script:
     - make include/vg_git_version.hpp
-    - docker buildx build --push --build-arg THREADS=8 -t "quay.io/vgteam/vg:ci-${CI_PIPELINE_IID}-${CI_COMMIT_SHA}" -f Dockerfile .
+    - docker buildx build --push --build-arg THREADS=8 --target run -t "quay.io/vgteam/vg:ci-${CI_PIPELINE_IID}-${CI_COMMIT_SHA}" -f Dockerfile .
+    # Also run the tests
+    - docker buildx build --build-arg THREADS=8 --target test -f Dockerfile .
   variables:
     GIT_SUBMODULE_STRATEGY: recursive
     

From 276a02ae5127c2a1893c24cbc381f5dee33130e7 Mon Sep 17 00:00:00 2001
From: Adam Novak <anovak@soe.ucsc.edu>
Date: Tue, 2 Feb 2021 17:19:14 -0800
Subject: [PATCH 17/34] Set up Deployment and buildx create for emulated ARM

---
 .gitlab-ci.yml               |  2 +-
 vgci/buildkit-deployment.yml | 18 ++++++++++++++++++
 2 files changed, 19 insertions(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index e051ae26d07..6146273ccf2 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -81,7 +81,7 @@ build-job:
     - mkdir -p ~/.docker/cli-plugins/ ; curl -L https://github.com/docker/buildx/releases/download/v0.5.1/buildx-v0.5.1.linux-amd64 >  ~/.docker/cli-plugins/docker-buildx ; chmod u+x ~/.docker/cli-plugins/docker-buildx
     # Connect to the Kubernetes-based builder "buildkit"
     # See vgci/buildkit-deployment.yml
-    - docker buildx create --use --name=buildkit --platform=linux/amd64 --node=buildkit-amd64 --driver=kubernetes --driver-opt="nodeselector=kubernetes.io/arch=amd64"
+    - docker buildx create --use --name=buildkit --platform=linux/amd64,linux/arm64 --node=buildkit-amd64 --driver=kubernetes --driver-opt="nodeselector=kubernetes.io/arch=amd64"
     # Connect so we can upload our images
     - docker login -u "${CI_REGISTRY_USER}" -p "${CI_REGISTRY_PASSWORD}" "${CI_REGISTRY}"
   script:
diff --git a/vgci/buildkit-deployment.yml b/vgci/buildkit-deployment.yml
index c94e8c39e3c..fc70172e4d4 100644
--- a/vgci/buildkit-deployment.yml
+++ b/vgci/buildkit-deployment.yml
@@ -51,6 +51,24 @@ spec:
             cpu: 500m
             memory: "1Gi"
             ephemeral-storage: "10Gi"
+      - name: binfmt
+        # We need this to set up the emulators in the host kernel for running
+        # ARM binaries. This image tells the kernel to go looking for qemu when
+        # it finds an ARM binary.
+        image: tonistiigi/binfmt
+        imagePullPolicy: IfNotPresent
+        args: ["--install", "arm64,arm"]
+        resources:
+          requests:
+            cpu: 500m
+            memory: "1Gi"
+            ephemeral-storage: "10Gi"
+          limits:
+            cpu: 500m
+            memory: "1Gi"
+            ephemeral-storage: "10Gi"
+        securityContext:
+          privileged: true
       containers:
       - image: moby/buildkit:buildx-stable-1
         imagePullPolicy: IfNotPresent

From 925da88b2f14c0788a47fc727efb3c3424ff051f Mon Sep 17 00:00:00 2001
From: Adam Novak <anovak@soe.ucsc.edu>
Date: Tue, 2 Feb 2021 17:21:01 -0800
Subject: [PATCH 18/34] Ask for ARM build and test

---
 .gitlab-ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 6146273ccf2..fac0c7201e2 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -86,9 +86,9 @@ build-job:
     - docker login -u "${CI_REGISTRY_USER}" -p "${CI_REGISTRY_PASSWORD}" "${CI_REGISTRY}"
   script:
     - make include/vg_git_version.hpp
-    - docker buildx build --push --build-arg THREADS=8 --target run -t "quay.io/vgteam/vg:ci-${CI_PIPELINE_IID}-${CI_COMMIT_SHA}" -f Dockerfile .
+    - docker buildx build --platform=linux/amd64,linux/arm64 --build-arg THREADS=8 --target run --push -t "quay.io/vgteam/vg:ci-${CI_PIPELINE_IID}-${CI_COMMIT_SHA}" -f Dockerfile .
     # Also run the tests
-    - docker buildx build --build-arg THREADS=8 --target test -f Dockerfile .
+    - docker buildx build --platform=linux/amd64,linux/arm64 --build-arg THREADS=8 --target test -f Dockerfile .
   variables:
     GIT_SUBMODULE_STRATEGY: recursive
     

From 26d3d76b8caeb99e3a3983cc42aeb18c016c8703 Mon Sep 17 00:00:00 2001
From: Adam Novak <anovak@soe.ucsc.edu>
Date: Tue, 2 Feb 2021 17:45:03 -0800
Subject: [PATCH 19/34] Don't try and make ARM builds for nehalem

---
 Dockerfile | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 459267e6d67..ea15b21f145 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -12,6 +12,7 @@ ENV DEBCONF_NONINTERACTIVE_SEEN true
 
 FROM base AS build
 ARG THREADS=8
+ARG TARGETARCH
 
 RUN echo build > /stage.txt
 
@@ -39,13 +40,13 @@ RUN apt-get -qq -y update && apt-get -qq -y upgrade && apt-get -qq -y install \
 # Pre-build non-package dependencies
 COPY source_me.sh /vg/source_me.sh
 COPY deps /vg/deps
-# To increase portability of the docker image, set the target CPU architecture to
-# Nehalem (2008) rather than auto-detecting the build machine's CPU.
-# This has no AVX1, AVX2, or PCLMUL, but it does have SSE4.2.
-# UCSC has a Nehalem machine that we want to support.
-RUN sed -i s/march=native/march=nehalem/ deps/sdsl-lite/CMakeLists.txt
+# To increase portability of the docker image, when building for amd64, set the
+# target CPU architecture to Nehalem (2008) rather than auto-detecting the
+# build machine's CPU. This has no AVX1, AVX2, or PCLMUL, but it does have
+# SSE4.2. UCSC has a Nehalem machine that we want to support.
+RUN if [[ -z "${TARGETARCH}" || "${TARGETARCH}" -eq "amd64" ]] ; then sed -i s/march=native/march=nehalem/ deps/sdsl-lite/CMakeLists.txt; fi
 COPY Makefile /vg/Makefile
-RUN . ./source_me.sh && CXXFLAGS=" -march=nehalem " make -j $((THREADS < $(nproc) ? THREADS : $(nproc))) deps
+RUN . ./source_me.sh && CXXFLAGS="$(if [[ -z "${TARGETARCH}" || "${TARGETARCH}" -eq "amd64" ]] ; then echo " -march=nehalem "; fi)" make -j $((THREADS < $(nproc) ? THREADS : $(nproc))) deps
 
 # Bring in the rest of the build tree that we need
 COPY src /vg/src
@@ -57,7 +58,7 @@ COPY include /vg/include
 
 # Do the build. Trim down the resulting binary but make sure to include enough debug info for profiling.
 # Also pass the arch here
-RUN . ./source_me.sh && CXXFLAGS=" -march=nehalem " make -j $((THREADS < $(nproc) ? THREADS : $(nproc))) static && strip -d bin/vg
+RUN . ./source_me.sh && CXXFLAGS="$(if [[ -z "${TARGETARCH}" || "${TARGETARCH}" -eq "amd64" ]] ; then echo " -march=nehalem "; fi)" make -j $((THREADS < $(nproc) ? THREADS : $(nproc))) static && strip -d bin/vg
 
 ENV PATH /vg/bin:$PATH
 

From c05d13a3c757bd83775ffb939191d13ff2db0487 Mon Sep 17 00:00:00 2001
From: Adam Novak <anovak@soe.ucsc.edu>
Date: Wed, 3 Feb 2021 09:13:49 -0800
Subject: [PATCH 20/34] Commit index to try and work around #3185

---
 test/wiki-data/mock-hs37d5/data/hs37d5.fa.fai | 86 +++++++++++++++++++
 1 file changed, 86 insertions(+)
 create mode 100644 test/wiki-data/mock-hs37d5/data/hs37d5.fa.fai

diff --git a/test/wiki-data/mock-hs37d5/data/hs37d5.fa.fai b/test/wiki-data/mock-hs37d5/data/hs37d5.fa.fai
new file mode 100644
index 00000000000..ec4fea30fa9
--- /dev/null
+++ b/test/wiki-data/mock-hs37d5/data/hs37d5.fa.fai
@@ -0,0 +1,86 @@
+1	1200	52	60	61
+2	1200	1324	60	61
+3	1200	2596	60	61
+4	1200	3868	60	61
+5	1200	5140	60	61
+6	1200	6412	60	61
+7	1200	7684	60	61
+8	1200	8956	60	61
+9	1200	10228	60	61
+10	1200	11502	60	61
+11	1200	12776	60	61
+12	1200	14050	60	61
+13	1200	15324	60	61
+14	1200	16598	60	61
+15	1200	17872	60	61
+16	1200	19145	60	61
+17	1200	20418	60	61
+18	1200	21691	60	61
+19	1200	22964	60	61
+20	1200	24237	60	61
+21	1200	25510	60	61
+22	1200	26783	60	61
+X	1200	28055	60	61
+Y	1200	29332	60	61
+MT	1400	30630	70	71
+GL000207.1	1200	32111	60	61
+GL000226.1	1200	33393	60	61
+GL000229.1	1200	34675	60	61
+GL000231.1	1200	35957	60	61
+GL000210.1	1200	37239	60	61
+GL000239.1	1200	38521	60	61
+GL000235.1	1200	39803	60	61
+GL000201.1	1200	41085	60	61
+GL000247.1	1200	42367	60	61
+GL000245.1	1200	43649	60	61
+GL000197.1	1200	44931	60	61
+GL000203.1	1200	46213	60	61
+GL000246.1	1200	47495	60	61
+GL000249.1	1200	48777	60	61
+GL000196.1	1200	50059	60	61
+GL000248.1	1200	51341	60	61
+GL000244.1	1200	52623	60	61
+GL000238.1	1200	53905	60	61
+GL000202.1	1200	55187	60	61
+GL000234.1	1200	56469	60	61
+GL000232.1	1200	57751	60	61
+GL000206.1	1200	59033	60	61
+GL000240.1	1200	60315	60	61
+GL000236.1	1200	61597	60	61
+GL000241.1	1200	62879	60	61
+GL000243.1	1200	64161	60	61
+GL000242.1	1200	65443	60	61
+GL000230.1	1200	66725	60	61
+GL000237.1	1200	68007	60	61
+GL000233.1	1200	69289	60	61
+GL000204.1	1200	70571	60	61
+GL000198.1	1200	71853	60	61
+GL000208.1	1200	73135	60	61
+GL000191.1	1200	74418	60	61
+GL000227.1	1200	75701	60	61
+GL000228.1	1200	76984	60	61
+GL000214.1	1200	78267	60	61
+GL000221.1	1200	79550	60	61
+GL000209.1	1200	80833	60	61
+GL000218.1	1200	82116	60	61
+GL000220.1	1200	83399	60	61
+GL000213.1	1200	84682	60	61
+GL000211.1	1200	85965	60	61
+GL000199.1	1200	87248	60	61
+GL000217.1	1200	88531	60	61
+GL000216.1	1200	89814	60	61
+GL000215.1	1200	91097	60	61
+GL000205.1	1200	92380	60	61
+GL000219.1	1200	93663	60	61
+GL000224.1	1200	94946	60	61
+GL000223.1	1200	96229	60	61
+GL000195.1	1200	97512	60	61
+GL000212.1	1200	98795	60	61
+GL000222.1	1200	100078	60	61
+GL000200.1	1200	101361	60	61
+GL000193.1	1200	102644	60	61
+GL000194.1	1200	103927	60	61
+GL000225.1	1200	105210	60	61
+GL000192.1	1200	106493	60	61
+NC_007605	1200	107724	60	61
+hs37d5	1200	108952	60	61

From 85e686dddf9f90c69353a33b3d4bd05b4ba4582a Mon Sep 17 00:00:00 2001
From: Adam Novak <anovak@soe.ucsc.edu>
Date: Wed, 3 Feb 2021 09:18:53 -0800
Subject: [PATCH 21/34] Make the test container actually run tests

---
 Dockerfile | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index ea15b21f145..46b8a9e089c 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -71,7 +71,8 @@ RUN echo test > /stage.txt
 # Fail if any non-portable instructions were used
 RUN /bin/bash -e -c 'if objdump -d /vg/bin/vg | grep vperm2i128 ; then exit 1 ; else exit 0 ; fi'
 # Run tests in the middle so the final container that gets tagged is the run container.
-RUN export OMP_NUM_THREADS=$((THREADS < $(nproc) ? THREADS : $(nproc))) make test
+# Tests may not actually be run by smart builders like buildkit.
+RUN /bin/bash -e -c "export OMP_NUM_THREADS=$((THREADS < $(nproc) ? THREADS : $(nproc))); make test"
 
 
 ############################################################################################

From fd946abcb14f12e2199f853450b78a62f2a1b182 Mon Sep 17 00:00:00 2001
From: Adam Novak <anovak@soe.ucsc.edu>
Date: Wed, 3 Feb 2021 09:23:28 -0800
Subject: [PATCH 22/34] Move the slow ARM container build alongside the other
 slow tests

---
 .gitlab-ci.yml | 31 +++++++++++++++++++++++++++----
 1 file changed, 27 insertions(+), 4 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index fac0c7201e2..00c325c0ae0 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -86,13 +86,36 @@ build-job:
     - docker login -u "${CI_REGISTRY_USER}" -p "${CI_REGISTRY_PASSWORD}" "${CI_REGISTRY}"
   script:
     - make include/vg_git_version.hpp
-    - docker buildx build --platform=linux/amd64,linux/arm64 --build-arg THREADS=8 --target run --push -t "quay.io/vgteam/vg:ci-${CI_PIPELINE_IID}-${CI_COMMIT_SHA}" -f Dockerfile .
+    - docker buildx build --platform=linux/amd64 --build-arg THREADS=8 --target run --push -t "quay.io/vgteam/vg:ci-${CI_PIPELINE_IID}-${CI_COMMIT_SHA}" -f Dockerfile .
     # Also run the tests
-    - docker buildx build --platform=linux/amd64,linux/arm64 --build-arg THREADS=8 --target test -f Dockerfile .
+    - docker buildx build --platform=linux/amd64 --build-arg THREADS=8 --target test -f Dockerfile .
   variables:
     GIT_SUBMODULE_STRATEGY: recursive
-    
-# We define a second follow-on phase to run the tests
+
+# The arm container build takes like 90 minutes, so we don't want to run it
+# before the main test phase where the other long tests live.
+arm-build-job:
+  stage: test
+  before_script:
+    # Don't bother starting the Docker daemon or installing much
+    - which docker || (sudo apt-get -q -y update && sudo apt-get -q -y install --no-upgrade docker.io)
+    # Get buildx
+    - mkdir -p ~/.docker/cli-plugins/ ; curl -L https://github.com/docker/buildx/releases/download/v0.5.1/buildx-v0.5.1.linux-amd64 >  ~/.docker/cli-plugins/docker-buildx ; chmod u+x ~/.docker/cli-plugins/docker-buildx
+    # Connect to the Kubernetes-based builder "buildkit"
+    # See vgci/buildkit-deployment.yml
+    - docker buildx create --use --name=buildkit --platform=linux/amd64,linux/arm64 --node=buildkit-amd64 --driver=kubernetes --driver-opt="nodeselector=kubernetes.io/arch=amd64"
+    # Connect so we can upload our images
+    - docker login -u "${CI_REGISTRY_USER}" -p "${CI_REGISTRY_PASSWORD}" "${CI_REGISTRY}"
+  script:
+    - make include/vg_git_version.hpp
+    # Build the arm container (emulated!)
+    - docker buildx build --platform=linux/arm64 --build-arg THREADS=8 --target run --push -t "quay.io/vgteam/vg:ci-${CI_PIPELINE_IID}-${CI_COMMIT_SHA}" -f Dockerfile .
+    # Also run the tests (emulated!)
+    - docker buildx build --platform=linux/arm64 --build-arg THREADS=8 --target test -f Dockerfile .
+  variables:
+    GIT_SUBMODULE_STRATEGY: recursive
+
+# We also run the toil-vg/pytest-based tests
 # Note that WE ONLY RUN TESTS LISTED IN vgci/test-list.txt
 test-job:
   stage: test

From 2d71b689d32f7c37e716fd3f50ba6996415fdc00 Mon Sep 17 00:00:00 2001
From: Adam Novak <anovak@soe.ucsc.edu>
Date: Wed, 3 Feb 2021 10:02:49 -0800
Subject: [PATCH 23/34] Ship 20.04 in the container so we have the right npm to
 install txm to run the tests

---
 Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 46b8a9e089c..cb61f3a5fa1 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,5 +1,5 @@
 # Multi-container Dockerfile for build and run containers for vg
-FROM ubuntu:18.04 AS base
+FROM ubuntu:20.04 AS base
 MAINTAINER vgteam
 
 RUN echo base > /stage.txt

From 955dd8c258626a65d2a9ca9602acce1dbf8544dc Mon Sep 17 00:00:00 2001
From: Adam Novak <anovak@soe.ucsc.edu>
Date: Wed, 3 Feb 2021 10:38:46 -0800
Subject: [PATCH 24/34] Allocate more cache space and try to keep it clean

---
 .gitlab-ci.yml               |  4 ++++
 vgci/buildkit-deployment.yml | 25 ++++++++++++++++++++++---
 2 files changed, 26 insertions(+), 3 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 00c325c0ae0..f73990c59e0 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -82,6 +82,8 @@ build-job:
     # Connect to the Kubernetes-based builder "buildkit"
     # See vgci/buildkit-deployment.yml
     - docker buildx create --use --name=buildkit --platform=linux/amd64,linux/arm64 --node=buildkit-amd64 --driver=kubernetes --driver-opt="nodeselector=kubernetes.io/arch=amd64"
+    # Prune down build cache to make space
+    - docker buildx prune --all --keep-storage 80G
     # Connect so we can upload our images
     - docker login -u "${CI_REGISTRY_USER}" -p "${CI_REGISTRY_PASSWORD}" "${CI_REGISTRY}"
   script:
@@ -104,6 +106,8 @@ arm-build-job:
     # Connect to the Kubernetes-based builder "buildkit"
     # See vgci/buildkit-deployment.yml
     - docker buildx create --use --name=buildkit --platform=linux/amd64,linux/arm64 --node=buildkit-amd64 --driver=kubernetes --driver-opt="nodeselector=kubernetes.io/arch=amd64"
+    # Prune down build cache to make space
+    - docker buildx prune --all --keep-storage 80G
     # Connect so we can upload our images
     - docker login -u "${CI_REGISTRY_USER}" -p "${CI_REGISTRY_PASSWORD}" "${CI_REGISTRY}"
   script:
diff --git a/vgci/buildkit-deployment.yml b/vgci/buildkit-deployment.yml
index fc70172e4d4..1db768665bd 100644
--- a/vgci/buildkit-deployment.yml
+++ b/vgci/buildkit-deployment.yml
@@ -35,7 +35,26 @@ spec:
       - name: configure
         image: moby/buildkit:buildx-stable-1
         imagePullPolicy: IfNotPresent
-        command: [/bin/sh, "-c", 'printf "[registry.\"docker.io\"]\nmirrors = [\"${DOCKER_HUB_MIRROR#*://}\"]\n[registry.\"${DOCKER_HUB_MIRROR#*://}\"]\nhttp = true\ninsecure = true\n" | tee /etc/buildkit/buildkitd.toml']
+        # Set up to GC any container data over 80 GB.
+        # In the background? See https://github.com/moby/buildkit/issues/1962
+        command:
+          - /bin/sh
+          - -c
+          - |
+            cat >/etc/buildkit/buildkitd.toml <<END
+              [registry."docker.io"]
+              mirrors = ["${DOCKER_HUB_MIRROR#*://}"]
+              [registry."${DOCKER_HUB_MIRROR#*://}"]
+              http = true
+              insecure = true
+              [worker.oci]
+              enabled = true
+              gc = true
+              gckeepstorage = 85899345920
+              [[worker.oci.gcpolicy]]
+              all = true
+              keepBytes = 85899345920
+            END
         volumeMounts:
         - name: buildkitconf
           mountPath: "/etc/buildkit"
@@ -91,11 +110,11 @@ spec:
           requests:
             cpu: 8000m
             memory: "24Gi"
-            ephemeral-storage: "30Gi"
+            ephemeral-storage: "100Gi"
           limits:
             cpu: 8000m
             memory: "24Gi"
-            ephemeral-storage: "30Gi"
+            ephemeral-storage: "100Gi"
         securityContext:
           privileged: true
         terminationMessagePath: /dev/termination-log

From 2eaa6d6885a111785e785b24dcdbd075769ea05a Mon Sep 17 00:00:00 2001
From: Adam Novak <anovak@soe.ucsc.edu>
Date: Wed, 3 Feb 2021 10:45:33 -0800
Subject: [PATCH 25/34] Try caching to and from Quay

---
 .gitlab-ci.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index f73990c59e0..6d63249e58f 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -88,9 +88,9 @@ build-job:
     - docker login -u "${CI_REGISTRY_USER}" -p "${CI_REGISTRY_PASSWORD}" "${CI_REGISTRY}"
   script:
     - make include/vg_git_version.hpp
-    - docker buildx build --platform=linux/amd64 --build-arg THREADS=8 --target run --push -t "quay.io/vgteam/vg:ci-${CI_PIPELINE_IID}-${CI_COMMIT_SHA}" -f Dockerfile .
+    - docker buildx build --platform=linux/amd64 --cache-to=type=registry,ref=quay.io/vgteam/vg --cache-from=type=registry,ref=quay.io/vgteam/vg --build-arg THREADS=8 --target run --push -t "quay.io/vgteam/vg:ci-${CI_PIPELINE_IID}-${CI_COMMIT_SHA}" -f Dockerfile .
     # Also run the tests
-    - docker buildx build --platform=linux/amd64 --build-arg THREADS=8 --target test -f Dockerfile .
+    - docker buildx build --platform=linux/amd64 --cache-to=type=registry,ref=quay.io/vgteam/vg --cache-from=type=registry,ref=quay.io/vgteam/vg --build-arg THREADS=8 --target test -f Dockerfile .
   variables:
     GIT_SUBMODULE_STRATEGY: recursive
 
@@ -113,9 +113,9 @@ arm-build-job:
   script:
     - make include/vg_git_version.hpp
     # Build the arm container (emulated!)
-    - docker buildx build --platform=linux/arm64 --build-arg THREADS=8 --target run --push -t "quay.io/vgteam/vg:ci-${CI_PIPELINE_IID}-${CI_COMMIT_SHA}" -f Dockerfile .
+    - docker buildx build --platform=linux/arm64 --cache-to=type=registry,ref=quay.io/vgteam/vg --cache-from=type=registry,ref=quay.io/vgteam/vg --build-arg THREADS=8 --target run --push -t "quay.io/vgteam/vg:ci-${CI_PIPELINE_IID}-${CI_COMMIT_SHA}" -f Dockerfile .
     # Also run the tests (emulated!)
-    - docker buildx build --platform=linux/arm64 --build-arg THREADS=8 --target test -f Dockerfile .
+    - docker buildx build --platform=linux/arm64 --cache-to=type=registry,ref=quay.io/vgteam/vg --cache-from=type=registry,ref=quay.io/vgteam/vg --build-arg THREADS=8 --target test -f Dockerfile .
   variables:
     GIT_SUBMODULE_STRATEGY: recursive
 

From 6900c9a04f1095cb8bacb2a3ff2d87465f48aa9a Mon Sep 17 00:00:00 2001
From: Adam Novak <anovak@soe.ucsc.edu>
Date: Wed, 3 Feb 2021 10:47:47 -0800
Subject: [PATCH 26/34] Drop old libssl1.0.0 that Ubuntu 20.04 lacks

---
 Dockerfile | 1 -
 1 file changed, 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index cb61f3a5fa1..c5f78a9b4d2 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -100,7 +100,6 @@ RUN ls -lah /vg && \
     fontconfig-config \
     awscli \
     binutils \
-    libssl1.0.0 \
     libpython2.7 \
     libperl-dev \
     libelf1 \

From 5c43c5c7597b8c838fc8ddf4a02335e615d73bf3 Mon Sep 17 00:00:00 2001
From: Adam Novak <anovak@soe.ucsc.edu>
Date: Wed, 3 Feb 2021 10:55:10 -0800
Subject: [PATCH 27/34] Don't try to prune off everything

---
 .gitlab-ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 6d63249e58f..21616f2218f 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -83,7 +83,7 @@ build-job:
     # See vgci/buildkit-deployment.yml
     - docker buildx create --use --name=buildkit --platform=linux/amd64,linux/arm64 --node=buildkit-amd64 --driver=kubernetes --driver-opt="nodeselector=kubernetes.io/arch=amd64"
     # Prune down build cache to make space
-    - docker buildx prune --all --keep-storage 80G
+    - docker buildx prune --keep-storage 80G
     # Connect so we can upload our images
     - docker login -u "${CI_REGISTRY_USER}" -p "${CI_REGISTRY_PASSWORD}" "${CI_REGISTRY}"
   script:
@@ -107,7 +107,7 @@ arm-build-job:
     # See vgci/buildkit-deployment.yml
     - docker buildx create --use --name=buildkit --platform=linux/amd64,linux/arm64 --node=buildkit-amd64 --driver=kubernetes --driver-opt="nodeselector=kubernetes.io/arch=amd64"
     # Prune down build cache to make space
-    - docker buildx prune --all --keep-storage 80G
+    - docker buildx prune --keep-storage 80G
     # Connect so we can upload our images
     - docker login -u "${CI_REGISTRY_USER}" -p "${CI_REGISTRY_PASSWORD}" "${CI_REGISTRY}"
   script:

From 202cd8045b450f6f98c322ec71b34cc7d8cf141f Mon Sep 17 00:00:00 2001
From: Adam Novak <anovak@soe.ucsc.edu>
Date: Wed, 3 Feb 2021 11:11:28 -0800
Subject: [PATCH 28/34] Remove bashism conditionals

---
 Dockerfile | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index c5f78a9b4d2..1abb857e5e5 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -44,9 +44,9 @@ COPY deps /vg/deps
 # target CPU architecture to Nehalem (2008) rather than auto-detecting the
 # build machine's CPU. This has no AVX1, AVX2, or PCLMUL, but it does have
 # SSE4.2. UCSC has a Nehalem machine that we want to support.
-RUN if [[ -z "${TARGETARCH}" || "${TARGETARCH}" -eq "amd64" ]] ; then sed -i s/march=native/march=nehalem/ deps/sdsl-lite/CMakeLists.txt; fi
+RUN if [ -z "${TARGETARCH}" ] || [ "${TARGETARCH}" -eq "amd64" ] ; then sed -i s/march=native/march=nehalem/ deps/sdsl-lite/CMakeLists.txt; fi
 COPY Makefile /vg/Makefile
-RUN . ./source_me.sh && CXXFLAGS="$(if [[ -z "${TARGETARCH}" || "${TARGETARCH}" -eq "amd64" ]] ; then echo " -march=nehalem "; fi)" make -j $((THREADS < $(nproc) ? THREADS : $(nproc))) deps
+RUN . ./source_me.sh && CXXFLAGS="$(if [ -z "${TARGETARCH}" ] || [ "${TARGETARCH}" -eq "amd64" ] ; then echo " -march=nehalem "; fi)" make -j $((THREADS < $(nproc) ? THREADS : $(nproc))) deps
 
 # Bring in the rest of the build tree that we need
 COPY src /vg/src
@@ -58,7 +58,7 @@ COPY include /vg/include
 
 # Do the build. Trim down the resulting binary but make sure to include enough debug info for profiling.
 # Also pass the arch here
-RUN . ./source_me.sh && CXXFLAGS="$(if [[ -z "${TARGETARCH}" || "${TARGETARCH}" -eq "amd64" ]] ; then echo " -march=nehalem "; fi)" make -j $((THREADS < $(nproc) ? THREADS : $(nproc))) static && strip -d bin/vg
+RUN . ./source_me.sh && CXXFLAGS="$(if [ -z "${TARGETARCH}" ] || [ "${TARGETARCH}" -eq "amd64" ] ; then echo " -march=nehalem "; fi)" make -j $((THREADS < $(nproc) ? THREADS : $(nproc))) static && strip -d bin/vg
 
 ENV PATH /vg/bin:$PATH
 

From 3c1f9fd348f9514616dca765690f9bd324bd26ac Mon Sep 17 00:00:00 2001
From: Adam Novak <anovak@soe.ucsc.edu>
Date: Wed, 3 Feb 2021 11:30:17 -0800
Subject: [PATCH 29/34] Drop Travis build status badge

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 876e369a55e..5b916a70bf0 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,7 @@
 <!-- !test program bash -eo pipefail -->
 # vg
 
-[![Join the chat at https://gitter.im/vgteam/vg](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/vgteam/vg?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) [![Latest Release](https://img.shields.io/github/release/vgteam/vg.svg)](https://github.com/vgteam/vg/releases/latest) [![Build Status](https://travis-ci.org/vgteam/vg.svg?branch=master)](https://travis-ci.org/vgteam/vg) [![Performance Report](https://img.shields.io/badge/performance-report-brightgreen.svg)](https://vg-data.s3.amazonaws.com/vg_ci/vgci_reports/branch/master/index.html) 
+[![Join the chat at https://gitter.im/vgteam/vg](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/vgteam/vg?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) [![Latest Release](https://img.shields.io/github/release/vgteam/vg.svg)](https://github.com/vgteam/vg/releases/latest) [![Performance Report](https://img.shields.io/badge/performance-report-brightgreen.svg)](https://vg-data.s3.amazonaws.com/vg_ci/vgci_reports/branch/master/index.html) 
 [![Doxygen API Documentation](https://img.shields.io/badge/doxygen-docs-brightgreen.svg)](https://vgteam.github.io/vg/)
 
 ## variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods

From 20d068e0dc1d821a8dfa2ed26c58524279f7f2b0 Mon Sep 17 00:00:00 2001
From: Adam Novak <anovak@soe.ucsc.edu>
Date: Wed, 3 Feb 2021 11:32:15 -0800
Subject: [PATCH 30/34] Don't cache from/to Quay because it won't accept a
 cache.

---
 .gitlab-ci.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 21616f2218f..bf38b721aea 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -88,9 +88,9 @@ build-job:
     - docker login -u "${CI_REGISTRY_USER}" -p "${CI_REGISTRY_PASSWORD}" "${CI_REGISTRY}"
   script:
     - make include/vg_git_version.hpp
-    - docker buildx build --platform=linux/amd64 --cache-to=type=registry,ref=quay.io/vgteam/vg --cache-from=type=registry,ref=quay.io/vgteam/vg --build-arg THREADS=8 --target run --push -t "quay.io/vgteam/vg:ci-${CI_PIPELINE_IID}-${CI_COMMIT_SHA}" -f Dockerfile .
+    - docker buildx build --platform=linux/amd64 --build-arg THREADS=8 --target run --push -t "quay.io/vgteam/vg:ci-${CI_PIPELINE_IID}-${CI_COMMIT_SHA}" -f Dockerfile .
     # Also run the tests
-    - docker buildx build --platform=linux/amd64 --cache-to=type=registry,ref=quay.io/vgteam/vg --cache-from=type=registry,ref=quay.io/vgteam/vg --build-arg THREADS=8 --target test -f Dockerfile .
+    - docker buildx build --platform=linux/amd64 --build-arg THREADS=8 --target test -f Dockerfile .
   variables:
     GIT_SUBMODULE_STRATEGY: recursive
 
@@ -113,9 +113,9 @@ arm-build-job:
   script:
     - make include/vg_git_version.hpp
     # Build the arm container (emulated!)
-    - docker buildx build --platform=linux/arm64 --cache-to=type=registry,ref=quay.io/vgteam/vg --cache-from=type=registry,ref=quay.io/vgteam/vg --build-arg THREADS=8 --target run --push -t "quay.io/vgteam/vg:ci-${CI_PIPELINE_IID}-${CI_COMMIT_SHA}" -f Dockerfile .
+    - docker buildx build --platform=linux/arm64 --build-arg THREADS=8 --target run --push -t "quay.io/vgteam/vg:ci-${CI_PIPELINE_IID}-${CI_COMMIT_SHA}" -f Dockerfile .
     # Also run the tests (emulated!)
-    - docker buildx build --platform=linux/arm64 --cache-to=type=registry,ref=quay.io/vgteam/vg --cache-from=type=registry,ref=quay.io/vgteam/vg --build-arg THREADS=8 --target test -f Dockerfile .
+    - docker buildx build --platform=linux/arm64 --build-arg THREADS=8 --target test -f Dockerfile .
   variables:
     GIT_SUBMODULE_STRATEGY: recursive
 

From 3c0cd69b3061492968b48292f4165cffa2f16360 Mon Sep 17 00:00:00 2001
From: Adam Novak <anovak@soe.ucsc.edu>
Date: Wed, 3 Feb 2021 12:13:19 -0800
Subject: [PATCH 31/34] Make sure to ship the README

---
 Dockerfile | 17 ++++++++++++-----
 1 file changed, 12 insertions(+), 5 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 1abb857e5e5..354d21dc19a 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -48,11 +48,8 @@ RUN if [ -z "${TARGETARCH}" ] || [ "${TARGETARCH}" -eq "amd64" ] ; then sed -i s
 COPY Makefile /vg/Makefile
 RUN . ./source_me.sh && CXXFLAGS="$(if [ -z "${TARGETARCH}" ] || [ "${TARGETARCH}" -eq "amd64" ] ; then echo " -march=nehalem "; fi)" make -j $((THREADS < $(nproc) ? THREADS : $(nproc))) deps
 
-# Bring in the rest of the build tree that we need
+# Bring in the sources, which we need in order to build
 COPY src /vg/src
-COPY test /vg/test
-COPY doc /vg/doc
-COPY scripts /vg/scripts
 # Bring in any includes we pre-made, like the git version
 COPY include /vg/include
 
@@ -60,6 +57,9 @@ COPY include /vg/include
 # Also pass the arch here
 RUN . ./source_me.sh && CXXFLAGS="$(if [ -z "${TARGETARCH}" ] || [ "${TARGETARCH}" -eq "amd64" ] ; then echo " -march=nehalem "; fi)" make -j $((THREADS < $(nproc) ? THREADS : $(nproc))) static && strip -d bin/vg
 
+# Ship the scripts
+COPY scripts /vg/scripts
+
 ENV PATH /vg/bin:$PATH
 
 ############################################################################################
@@ -70,6 +70,13 @@ RUN echo test > /stage.txt
 
 # Fail if any non-portable instructions were used
 RUN /bin/bash -e -c 'if objdump -d /vg/bin/vg | grep vperm2i128 ; then exit 1 ; else exit 0 ; fi'
+
+# Bring in the tests and docs, which have doctests
+COPY test /vg/test
+COPY doc /vg/doc
+# We test the README so bring it along.
+COPY README.md /vg/
+
 # Run tests in the middle so the final container that gets tagged is the run container.
 # Tests may not actually be run by smart builders like buildkit.
 RUN /bin/bash -e -c "export OMP_NUM_THREADS=$((THREADS < $(nproc) ? THREADS : $(nproc))); make test"
@@ -117,7 +124,7 @@ COPY --from=build /vg/bin/vg /vg/bin/
 
 COPY --from=build /vg/scripts/* /vg/scripts/
 # Make sure we have the flame graph scripts so we can do self-profiling
-COPY deps/FlameGraph /vg/deps/FlameGraph
+COPY --from=build /vg/deps/FlameGraph /vg/deps/FlameGraph
 
 ENV PATH /vg/bin:$PATH
 

From 2144f4cd3ba9e7ebaa1c5560a1a294b81b5efcc6 Mon Sep 17 00:00:00 2001
From: Adam Novak <anovak@soe.ucsc.edu>
Date: Wed, 3 Feb 2021 12:42:26 -0800
Subject: [PATCH 32/34] Build o files separately and use real sh string
 comparison

---
 Dockerfile | 19 +++++++++++++------
 Makefile   | 19 +++++++++++++------
 2 files changed, 26 insertions(+), 12 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 354d21dc19a..3b7efa84a04 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -37,25 +37,32 @@ RUN apt-get -qq -y update && apt-get -qq -y upgrade && apt-get -qq -y install \
     libcairo2-dev libpixman-1-dev libffi-dev libcairo-dev libprotobuf-dev libboost-all-dev
 ###DEPS_END###
 
-# Pre-build non-package dependencies
+# Prepare to build submodule dependencies
 COPY source_me.sh /vg/source_me.sh
 COPY deps /vg/deps
 # To increase portability of the docker image, when building for amd64, set the
 # target CPU architecture to Nehalem (2008) rather than auto-detecting the
 # build machine's CPU. This has no AVX1, AVX2, or PCLMUL, but it does have
 # SSE4.2. UCSC has a Nehalem machine that we want to support.
-RUN if [ -z "${TARGETARCH}" ] || [ "${TARGETARCH}" -eq "amd64" ] ; then sed -i s/march=native/march=nehalem/ deps/sdsl-lite/CMakeLists.txt; fi
+RUN if [ -z "${TARGETARCH}" ] || [ "${TARGETARCH}" = "amd64" ] ; then sed -i s/march=native/march=nehalem/ deps/sdsl-lite/CMakeLists.txt; fi
+# Clear any CMake caches in case we are building from someone's checkout
+RUN find . -name CMakeCache.txt | xargs rm
+# Build the dependencies
 COPY Makefile /vg/Makefile
-RUN . ./source_me.sh && CXXFLAGS="$(if [ -z "${TARGETARCH}" ] || [ "${TARGETARCH}" -eq "amd64" ] ; then echo " -march=nehalem "; fi)" make -j $((THREADS < $(nproc) ? THREADS : $(nproc))) deps
+RUN . ./source_me.sh && CXXFLAGS="$(if [ -z "${TARGETARCH}" ] || [ "${TARGETARCH}" = "amd64" ] ; then echo " -march=nehalem "; fi)" make -j $((THREADS < $(nproc) ? THREADS : $(nproc))) deps
 
 # Bring in the sources, which we need in order to build
 COPY src /vg/src
+
+# Build all the object files for vg, but don't link.
+# Also pass the arch here
+RUN . ./source_me.sh && CXXFLAGS="$(if [ -z "${TARGETARCH}" ] || [ "${TARGETARCH}" = "amd64" ] ; then echo " -march=nehalem "; fi)" make -j $((THREADS < $(nproc) ? THREADS : $(nproc))) objs
+
 # Bring in any includes we pre-made, like the git version
 COPY include /vg/include
 
-# Do the build. Trim down the resulting binary but make sure to include enough debug info for profiling.
-# Also pass the arch here
-RUN . ./source_me.sh && CXXFLAGS="$(if [ -z "${TARGETARCH}" ] || [ "${TARGETARCH}" -eq "amd64" ] ; then echo " -march=nehalem "; fi)" make -j $((THREADS < $(nproc) ? THREADS : $(nproc))) static && strip -d bin/vg
+# Do the final build and link, knowing the version. Trim down the resulting binary but make sure to include enough debug info for profiling.
+RUN . ./source_me.sh && CXXFLAGS="$(if [ -z "${TARGETARCH}" ] || [ "${TARGETARCH}" = "amd64" ] ; then echo " -march=nehalem "; fi)" make -j $((THREADS < $(nproc) ? THREADS : $(nproc))) static && strip -d bin/vg
 
 # Ship the scripts
 COPY scripts /vg/scripts
diff --git a/Makefile b/Makefile
index 2c107568170..21b35e73e41 100644
--- a/Makefile
+++ b/Makefile
@@ -358,10 +358,21 @@ ifneq ($(shell uname -s),Darwin)
 	LD_LIB_FLAGS += -ljemalloc
 endif
 
-.PHONY: clean get-deps deps test set-path static static-docker docs man .pre-build .check-environment .check-git .no-git 
+.PHONY: clean get-deps deps test set-path objs static static-docker docs man .pre-build .check-environment .check-git .no-git 
+
+# Aggregate all libvg deps, and exe deps other than libvg
+LIBVG_DEPS = $(OBJ) $(ALGORITHMS_OBJ) $(IO_OBJ) $(DEP_OBJ) $(DEPS)
+EXE_DEPS = $(OBJ_DIR)/main.o $(UNITTEST_OBJ) $(SUBCOMMAND_OBJ) $(CONFIGURATION_OBJ) $(DEPS) $(LINK_DEPS)
+
+# We have a target we can build to do everything but link the library and executable
+objs: $(LIBVG_DEPS) $(EXE_DEPS)
+
+$(LIB_DIR)/libvg.a: $(LIBVG_DEPS)
+	rm -f $@
+	ar rs $@ $(OBJ) $(ALGORITHMS_OBJ) $(IO_OBJ) $(DEP_OBJ)
 
 # For a normal dynamic build we remove the static build marker
-$(BIN_DIR)/$(EXE): $(OBJ_DIR)/main.o $(LIB_DIR)/libvg.a $(UNITTEST_OBJ) $(SUBCOMMAND_OBJ) $(CONFIGURATION_OBJ) $(DEPS) $(LINK_DEPS)
+$(BIN_DIR)/$(EXE): $(LIB_DIR)/libvg.a $(EXE_DEPS)
 	-rm -f $(LIB_DIR)/vg_is_static
 	. ./source_me.sh && $(CXX) $(LDFLAGS) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$(EXE) $(OBJ_DIR)/main.o $(UNITTEST_OBJ) $(SUBCOMMAND_OBJ) $(CONFIGURATION_OBJ) -lvg $(LD_LIB_DIR_FLAGS) $(LD_LIB_FLAGS) $(START_STATIC) $(LD_STATIC_LIB_FLAGS) $(END_STATIC) $(LD_STATIC_LIB_DEPS) 
 # We keep a file that we touch on the last static build.
@@ -382,10 +393,6 @@ static-docker: static scripts/*
 	strip -d $(BIN_DIR)/$(EXE)
 	DOCKER_BUILDKIT=1 docker build . -f Dockerfile.static -t vg
 
-$(LIB_DIR)/libvg.a: $(OBJ) $(ALGORITHMS_OBJ) $(IO_OBJ) $(DEP_OBJ) $(DEPS)
-	rm -f $@
-	ar rs $@ $(OBJ) $(ALGORITHMS_OBJ) $(IO_OBJ) $(DEP_OBJ)
-
 # We have system-level deps to install
 # We want the One True Place for them to be in the Dockerfile.
 get-deps:

From e3c89c16f26d0d021c4d3e855c483bb2d3d50d44 Mon Sep 17 00:00:00 2001
From: Adam Novak <anovak@soe.ucsc.edu>
Date: Wed, 3 Feb 2021 13:23:49 -0800
Subject: [PATCH 33/34] Accept not having cmake caches

---
 Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 3b7efa84a04..651c7235dba 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -46,7 +46,7 @@ COPY deps /vg/deps
 # SSE4.2. UCSC has a Nehalem machine that we want to support.
 RUN if [ -z "${TARGETARCH}" ] || [ "${TARGETARCH}" = "amd64" ] ; then sed -i s/march=native/march=nehalem/ deps/sdsl-lite/CMakeLists.txt; fi
 # Clear any CMake caches in case we are building from someone's checkout
-RUN find . -name CMakeCache.txt | xargs rm
+RUN find . -name CMakeCache.txt | xargs rm -f
 # Build the dependencies
 COPY Makefile /vg/Makefile
 RUN . ./source_me.sh && CXXFLAGS="$(if [ -z "${TARGETARCH}" ] || [ "${TARGETARCH}" = "amd64" ] ; then echo " -march=nehalem "; fi)" make -j $((THREADS < $(nproc) ? THREADS : $(nproc))) deps

From cf4497cc059e61f365662bc5fc557ea388e06b01 Mon Sep 17 00:00:00 2001
From: Adam Novak <anovak@soe.ucsc.edu>
Date: Wed, 3 Feb 2021 14:51:56 -0800
Subject: [PATCH 34/34] Restrict arm tests to arm branches and expect failure

---
 .gitlab-ci.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index bf38b721aea..42e863df11a 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -96,8 +96,11 @@ build-job:
 
 # The arm container build takes like 90 minutes, so we don't want to run it
 # before the main test phase where the other long tests live.
+# They also don't pass yet.
 arm-build-job:
   stage: test
+  only:
+    - /^arm/
   before_script:
     # Don't bother starting the Docker daemon or installing much
     - which docker || (sudo apt-get -q -y update && sudo apt-get -q -y install --no-upgrade docker.io)
@@ -115,7 +118,8 @@ arm-build-job:
     # Build the arm container (emulated!)
     - docker buildx build --platform=linux/arm64 --build-arg THREADS=8 --target run --push -t "quay.io/vgteam/vg:ci-${CI_PIPELINE_IID}-${CI_COMMIT_SHA}" -f Dockerfile .
     # Also run the tests (emulated!)
-    - docker buildx build --platform=linux/arm64 --build-arg THREADS=8 --target test -f Dockerfile .
+    # But don't fail if they fail yet, because they don't yet actually work.
+    - docker buildx build --platform=linux/arm64 --build-arg THREADS=8 --target test -f Dockerfile . || true
   variables:
     GIT_SUBMODULE_STRATEGY: recursive