GW v0.10.0

.github/workflows/main.yml

@@ -5,14 +5,14 @@ on:
   pull_request:
 
 env:
-  version: 0.9.3
+  version: 0.10.0
 
 jobs:
   mingw:
    strategy:
      fail-fast: false
      matrix:
-       sys: [clang64, ucrt64]
+       sys: [ucrt64]  # clang64,
    name: ${{ matrix.sys }}
    runs-on: windows-latest
    defaults:
@@ -114,7 +114,7 @@ jobs:
         run: |
           sudo apt update
           sudo apt-get install dh-make build-essential debhelper dh-virtualenv
-          sudo apt-get install devscripts fakeroot debootstrap pbuilder autotools-dev
+          sudo apt-get install debugedit devscripts fakeroot debootstrap pbuilder autotools-dev
           sudo apt install zlib1g-dev libbz2-dev liblzma-dev libncurses5-dev libncursesw5-dev libssl-dev 
           sudo apt install libgl1-mesa-dev libfontconfig-dev libcurl4-openssl-dev libglfw3 libglfw3-dev
       - name: build
@@ -140,9 +140,10 @@ jobs:
           echo "LIBDEFLATE BUILT" && pwd
           cd ${BUILD_DIR}
 
-          wget -O htslib.tar.bz2 https://github.com/samtools/htslib/releases/download/1.17/htslib-1.17.tar.bz2
+          wget -O htslib.tar.bz2 https://github.com/samtools/htslib/releases/download/1.20/htslib-1.20.tar.bz2
           tar -xvf htslib.tar.bz2
-          mv htslib-1.17 htslib && rm htslib.tar.bz2 && cd htslib
+          mv htslib-1.20 htslib && rm htslib.tar.bz2 && cd htslib
+          sed -i 's/ -g -Wall/ -Wall/' Makefile  # strip debug information
           ./configure --enable-libcurl --enable-s3 --enable-lzma --enable-bz2 --with-libdeflate
           make -j3
           echo "HTSLIB BUILT" && pwd
@@ -164,21 +165,24 @@ jobs:
 
       - name: package
         run: |
-
           dh_make --single --createorig --packagename gw_${version} --email clealk@cardiff.ac.uk --yes --native
+
           printf "usr/bin/gw\nusr/share/icons/gw_icon.png\nusr/share/applications/gw.desktop\nusr/lib/gwhts/\nusr/lib/x86_64-linux-gnu/libglfw.so.3\nusr/lib/x86_64-linux-gnu/libglfw.so.3.3" > debian/install
 
           export LDFLAGS="$LDFLAGS -L./lib/skia/out/Release-x64 -L/usr/local/lib -L/usr/lib -L./usr/lib/gwhts -Wl,-rpath,'$ORIGIN/../lib/gwhts'"
+
           sed -i '/^Section/c\Section: Bioinformatics' debian/control
           sed -i '/^Homepage/c\Homepage: https://github.com/kcleal/gw' debian/control
-
           sed -i '/^Description/c\Description: Genome browser and variant annotation' debian/control
           sed -i '/<insert long/d' debian/control
+          printf "Conflicts: libglfw3 (<< 3.3)\nReplaces: libglfw3\n" >> debian/control
 
-          printf "Conflicts: libglfw3 (<< 3.3)\n" >> debian/control
-          printf "Replaces: libglfw3 \n" >> debian/control
+          # Override dh_shlibdeps to include /usr/lib/gwhts
+          printf '#!/usr/bin/make -f\n%%:\n\tdh $@\n\nclean:\n\tdh_clean\n\noverride_dh_shlibdeps:\n\tdh_shlibdeps -l/usr/lib/gwhts\n' > debian/rules
+          chmod +x debian/rules
 
-          dpkg-buildpackage
+          dpkg-buildpackage -us -uc
+
       - name: upload
         uses: actions/upload-artifact@v3
         with:

.gitignore

@@ -33,3 +33,9 @@
 /lib/libBigWig/bwValues.o
 /lib/libBigWig/bwWrite.o
 /lib/libBigWig/io.o
+/lib/libgw/
+libgw.so
+/libgw.dylib
+/gw.wasm
+/wasm_libs
+/src/plot_commands.o

.gw.ini

@@ -22,7 +22,7 @@ saccer3=https://github.com/kcleal/ref_genomes/releases/download/v0.1.0/sacCer3.f
 
 [general]
 theme=dark
-dimensions=3000x1000
+dimensions=1366x800
 indel_length=10
 ylim=50
 coverage=true
@@ -37,12 +37,16 @@ tabix_track_height=0.3
 font=Menlo
 font_size=14
 sv_arcs=true
+mods=false
+mods_qual_threshold=50
+session_file=
 
 [view_thresholds]
 soft_clip=20000
 small_indel=100000
 snp=500000
-edge_highlights=100000
+mod=250000
+edge_highlights=1000000
 variant_distance=100000
 low_memory=1500000
 

Makefile

@@ -9,11 +9,13 @@ debug: default
 
 # set system
 PLATFORM=
+UNAME_S := $(shell uname -s)
 ifeq ($(OS),Windows_NT)  # assume we are using msys2-ucrt64 env
     PLATFORM = "Windows"
 else
-    UNAME_S := $(shell uname -s)
-    ifeq ($(UNAME_S),Linux)
+    ifdef EMSCRIPTEN
+        PLATFORM = "Emscripten"
+    else ifeq ($(UNAME_S),Linux)
         PLATFORM = "Linux"
     else ifeq ($(UNAME_S),Darwin)
         ifeq ($(shell uname -m), arm64)
@@ -23,66 +25,63 @@ else
         endif
     endif
 endif
-
-# try and add conda environment
-ifdef CONDA_PREFIX
-    CPPFLAGS += -I$(CONDA_PREFIX)/include
-    LDFLAGS += -L$(CONDA_PREFIX)/lib
-endif
-
-# Options to use target htslib or skia
-ifdef HTSLIB
-    CPPFLAGS += -I$(HTSLIB)
-    LDFLAGS += -L$(HTSLIB)
+ifneq ($(PLATFORM),"Emscripten")
+    # try and add conda environment
+    ifdef CONDA_PREFIX
+        CPPFLAGS += -I$(CONDA_PREFIX)/include
+        LDFLAGS += -L$(CONDA_PREFIX)/lib
+    endif
+    ifdef HTSLIB # Options to use target htslib or skia
+        CPPFLAGS += -I$(HTSLIB)
+        LDFLAGS += -L$(HTSLIB)
+    endif
 endif
 
 SKIA ?= ""
+SKIA_PATH=""
 ifneq ($(PLATFORM), "Windows")
     ifneq ($(SKIA),"")
         CPPFLAGS += -I$(SKIA)
-        LDFLAGS += -L $(wildcard $(SKIA)/out/Rel*)
-    else ifeq ($(PLATFORM),"Darwin")
-        CPPFLAGS += -I./lib/skia
-        LDFLAGS += -L./lib/skia/out/Release-x64
+        SKIA_PATH = $(wildcard $(SKIA)/out/Rel*)
     else ifeq ($(PLATFORM),"Arm64")
         CPPFLAGS += -I./lib/skia
-        LDFLAGS += -L./lib/skia/out/Release-arm64
-    else
+        SKIA_PATH = ./lib/skia/out/Release-arm64
+    else ifeq ($(PLATFORM),"Emscripten")
+        CPPFLAGS += -I./wasm_libs/skia -I./wasm_libs/htslib
+        SKIA_PATH = ./wasm_libs/skia/out/canvaskit_wasm
+    else  # Darwin / Linux
     	CPPFLAGS += -I./lib/skia
-        LDFLAGS += -L./lib/skia/out/Release-x64
+        SKIA_PATH = ./lib/skia/out/Release-x64
+        LDFLAGS=
     endif
 endif
 
+LDFLAGS += -L$(SKIA_PATH)
 SKIA_LINK=""
 USE_GL ?= ""  # Else use EGL backend for Linux only
 
 prep:
 	@if [ "$(PLATFORM)" = "Darwin" ]; then \
 		SKIA_LINK=""; \
 		echo "Downloading pre-built skia for MacOS-Intel"; mkdir -p lib/skia; \
-		cd lib/skia && wget -O skia.zip "https://github.com/JetBrains/skia-build/releases/download/m93-87e8842e8c/Skia-m93-87e8842e8c-macos-Release-x64.zip" && unzip -o skia.zip && rm skia.zip && cd ../../; \
+		cd lib/skia && curl -L -o skia.zip "https://github.com/JetBrains/skia-build/releases/download/m93-87e8842e8c/Skia-m93-87e8842e8c-macos-Release-x64.zip" && unzip -o skia.zip && rm skia.zip && cd ../../; \
 	elif [ "$(PLATFORM)" = "Arm64" ]; then \
       	echo "Downloading pre-built skia for MacOS-Arm64"; mkdir -p lib/skia; \
-      	cd lib/skia && wget -O skia.tar.gz "https://github.com/kcleal/skia_build_arm64/releases/download/v0.0.1/skia.zip" && tar -xvf skia.tar.gz && rm skia.tar.gz && cd ../../; \
+      	cd lib/skia && curl -L -o skia.tar.gz "https://github.com/kcleal/skia_build_arm64/releases/download/v0.0.1/skia.zip" && tar -xvf skia.tar.gz && rm skia.tar.gz && cd ../../; \
 	elif [ "$(PLATFORM)" = "Linux" ] && [ "$(USE_GL)" = "1" ]; then \
 		echo "Downloading pre-built skia for Linux with GL"; mkdir -p lib/skia; \
-		cd lib/skia && wget -O skia.zip "https://github.com/JetBrains/skia-build/releases/download/m93-87e8842e8c/Skia-m93-87e8842e8c-linux-Release-x64.zip" && unzip -o skia.zip && rm skia.zip && cd ../../; \
+		cd lib/skia && curl -L -o skia.zip "https://github.com/JetBrains/skia-build/releases/download/m93-87e8842e8c/Skia-m93-87e8842e8c-linux-Release-x64.zip" && unzip -o skia.zip && rm skia.zip && cd ../../; \
 	elif [ "$(PLATFORM)" = "Linux" ]; then \
 		echo "Downloading pre-built skia for Linux with EGL"; mkdir -p lib/skia; \
-		cd lib/skia && wget -O skia.tar.gz "https://github.com/kcleal/skia_build_arm64/releases/download/v0.0.1/skia-m93-linux-Release-x64.tar.gz" && tar -xvf skia.tar.gz && rm skia.tar.gz && cd ../../; \
+		cd lib/skia && curl -L -o skia.tar.gz "https://github.com/kcleal/skia_build_arm64/releases/download/v0.0.1/skia-m93-linux-Release-x64.tar.gz" && tar -xvf skia.tar.gz && rm skia.tar.gz && cd ../../; \
 	fi
 
-
-CXXFLAGS += -Wall -std=c++17 -fno-common -fwrapv -fno-omit-frame-pointer -O3 -DNDEBUG
-
-CPPFLAGS += -I./lib/libBigWig -I./include -I./src -I.
-
-LDLIBS += -lskia -lm -ljpeg -lpng -lsvg -lhts -lfontconfig -lpthread
-
-
-
-# set platform flags and libs
-ifeq ($(PLATFORM),"Linux")
+CXXFLAGS += -Wall -std=c++17 -fno-common -fwrapv -fno-omit-frame-pointer -O3 -DNDEBUG -g
+LIBGW_INCLUDE=
+shared: LIBGW_INCLUDE=-I./libgw
+CPPFLAGS += -I./lib/libBigWig -I./include -I. $(LIBGW_INCLUDE) -I./src
+LDLIBS += -lskia -lm -ljpeg -lpng -lpthread
+ifeq ($(PLATFORM),"Linux")  # set platform flags and libs
     ifeq (${XDG_SESSION_TYPE},"wayland")  # wayland is untested!
         LDLIBS += -lwayland-client
     else
@@ -92,60 +91,72 @@ ifeq ($(PLATFORM),"Linux")
     CXXFLAGS += -D LINUX -D __STDC_FORMAT_MACROS
     LDFLAGS += -L/usr/local/lib
     # If installed from conda, glfw3 is named glfw, therefore if glfw3 is installed by another means use this:
-#     LDLIBS += -lGL -lfreetype -lfontconfig -luuid -lzlib -licu -ldl $(shell pkg-config --static --libs x11 xrandr xi xxf86vm glfw3)
+#    LDLIBS += -lGL -lfreetype -lfontconfig -luuid -lzlib -licu -ldl $(shell pkg-config --static --libs x11 xrandr xi xxf86vm glfw3)
 #    LDLIBS += -lEGL -lGLESv2 -lfreetype -lfontconfig -luuid -lz -lcurl -licu -ldl -lglfw #$(shell pkg-config --static --libs x11 xrandr xi xxf86vm glfw3)
-#    LDLIBS += -lGL -lfreetype -lfontconfig -luuid -lz -lcurl -licu -ldl -lglfw
     ifeq ($(USE_GL),"1")
         LDLIBS += -lGL
     else
         LDLIBS += -lEGL -lGLESv2
     endif
-    LDLIBS += -lfreetype -lfontconfig -luuid -lz -lcurl -licu -ldl -lglfw
-
+    LDLIBS += -lhts -lfreetype -luuid -lz -lcurl -licu -ldl -lglfw -lsvg -lfontconfig
 else ifeq ($(PLATFORM),"Darwin")
     CPPFLAGS += -I/usr/local/include
-    CXXFLAGS += -D OSX -stdlib=libc++ -arch x86_64 -fvisibility=hidden -mmacosx-version-min=10.15 -Wno-deprecated-declarations
+    CXXFLAGS += -D OSX -stdlib=libc++ -arch x86_64 -fvisibility=hidden -mmacosx-version-min=11 -Wno-deprecated-declarations
     LDFLAGS += -undefined dynamic_lookup -framework OpenGL -framework AppKit -framework ApplicationServices -mmacosx-version-min=10.15 -L/usr/local/lib
-    LDLIBS += -lglfw -lzlib -lcurl -licu -ldl
-
+    LDLIBS += -lhts -lglfw -lzlib -lcurl -licu -ldl -lsvg -lfontconfig
 else ifeq ($(PLATFORM),"Arm64")
     CPPFLAGS += -I/usr/local/include
-    CXXFLAGS += -D OSX -stdlib=libc++ -arch arm64 -fvisibility=hidden -mmacosx-version-min=10.15 -Wno-deprecated-declarations
+    CXXFLAGS += -D OSX -stdlib=libc++ -arch arm64 -fvisibility=hidden -mmacosx-version-min=11 -Wno-deprecated-declarations
     LDFLAGS += -undefined dynamic_lookup -framework OpenGL -framework AppKit -framework ApplicationServices -mmacosx-version-min=10.15 -L/usr/local/lib
-    LDLIBS += -lglfw -lzlib -lcurl -licu -ldl
-
+    LDLIBS += -lhts -lglfw -lzlib -lcurl -licu -ldl -lsvg -lfontconfig
 else ifeq ($(PLATFORM),"Windows")
     CXXFLAGS += -D WIN32
     CPPFLAGS += $(shell pkgconf -cflags skia) $(shell ncursesw6-config --cflags)
     LDLIBS += $(shell pkgconf -libs skia)
-    LDLIBS += -lharfbuzz-subset -lglfw3 -lcurl
+    LDLIBS += -lhts -lharfbuzz-subset -lglfw3 -lcurl -lsvg -lfontconfig
+else ifeq ($(PLATFORM),"Emscripten")
+    CPPFLAGS += -v --use-port=contrib.glfw3 -sUSE_ZLIB=1 -sUSE_FREETYPE=1 -sUSE_ICU=1  -I/usr/local/include
+    CFLAGS += -fPIC
+    CXXFLAGS += -DBUILDING_LIBGW -D__STDC_FORMAT_MACROS -fPIC
+    LDFLAGS += -v -L./wasm_libs/htslib -s RELOCATABLE=1 --no-entry -s STANDALONE_WASM
+    LDLIBS += -lwebgl.js -l:libhts.a
 endif
 
 OBJECTS = $(patsubst %.cpp, %.o, $(wildcard ./src/*.cpp))
 OBJECTS += $(patsubst %.c, %.o, $(wildcard ./lib/libBigWig/*.c))
 
 
-debug: CXXFLAGS += -g
 debug: LDFLAGS += -fsanitize=address -fsanitize=undefined
 
-$(TARGET): $(OBJECTS)
-	$(CXX) -g $(OBJECTS) $(LDFLAGS) $(LDLIBS) -o $@
+$(TARGET): $(OBJECTS)  # line 131
+	$(CXX) $(CXXFLAGS) $(OBJECTS) $(LDFLAGS) $(LDLIBS) -o $@
 
 
 clean:
 	-rm -f *.o ./src/*.o ./src/*.o.tmp ./lib/libBigWig/*.o
 	-rm -f $(TARGET)
-	-rm -rf libgw
+	-rm -rf libgw.* *.wasm
 
 
-SHARED_TARGET = libgw/libgw.so
-ifeq ($(PLATFORM),"Darwin")
-    SHARED_TARGET = libgw/libgw.dylib
+
+ifeq ($(UNAME_S),Linux)
+    SHARED_TARGET = libgw.so
+endif
+ifeq ($(UNAME_S),Darwin)
+    SHARED_TARGET = libgw.dylib
 endif
 
-shared: CXXFLAGS += -fPIC
+shared: CXXFLAGS += -fPIC -DBUILDING_LIBGW
+shared: CFLAGS += -fPIC
 shared: $(OBJECTS)
-	-mkdir -p libgw/include
-	-cp src/*.h libgw/include
-	-cp include/*.h libgw/include
-	$(CXX) $(OBJECTS) $(LDFLAGS) $(LDLIBS) -shared -o $(SHARED_TARGET)
+
+ifeq ($(UNAME_S),Darwin)
+	$(CXX) $(OBJECTS) $(LDFLAGS) $(LDLIBS) -dynamiclib -DBUILDING_LIBGW -o $(SHARED_TARGET)
+else
+	$(CXX) $(OBJECTS) $(LDFLAGS) $(LDLIBS) -shared -DBUILDING_LIBGW -o $(SHARED_TARGET)
+endif
+	-mkdir -p lib/libgw/include lib/libgw/out
+	-cp $(SKIA_PATH)/libskia.a lib/libgw/out
+	-cp src/*.h lib/libgw/include
+	-cp include/*.h* lib/libgw/include
+	-mv $(SHARED_TARGET) lib/libgw/out

deps/compile_wasm_libs.sh

@@ -0,0 +1,49 @@
+#!/bin/bash
+
+# Run this in the gw top-level directory (same as Makefile)
+# Also dont forget to source emsdk environment
+# source ~/Tools/emsdk/emsdk_env.sh
+
+emcc --version
+mkdir -p wasm_libs
+cd wasm_libs
+
+sudo apt-get install -y zlib1g-dev libbz2-dev libcurl4-gnutls-dev libssl-dev autoconf
+
+
+# Compile LZMA to WebAssembly
+LZMA_VERSION="5.2.5"
+curl -LO "https://tukaani.org/xz/xz-${LZMA_VERSION}.tar.gz"
+tar -xvf xz-${LZMA_VERSION}.tar.gz && rm xz*.gz
+cd xz-${LZMA_VERSION}
+emconfigure ./configure --disable-shared --disable-threads
+emmake make -j4 CFLAGS="-Oz -fPIC -s USE_PTHREADS=0 -s EXPORT_ALL=1 -s ASSERTIONS=1"
+cd ..
+
+
+# Run ./configure
+CFLAGS="-s USE_ZLIB=1 -s USE_BZIP2=1 ${CFLAGS_LZMA} -I./xz-${LZMA_VERSION}/src/liblzma/api/"
+LDFLAGS="$LDFLAGS_LZMA -L./xz-${LZMA_VERSION}/src/liblzma/.libs/"
+make clean
+autoheader
+autoconf
+emconfigure ./configure CFLAGS="$CFLAGS -fPIC" LDFLAGS="$LDFLAGS --relocatable"
+
+
+# Build htslib
+curl -L -o htslib.tar.bz2 https://github.com/samtools/htslib/releases/download/1.20/htslib-1.20.tar.bz2
+tar -xvf htslib.tar.bz2 && rm htslib.tar.bz2 && mv htslib-1.20 htslib
+cd htslib
+emmake make -j4 CC=emcc AR=emar \
+    CFLAGS="-O2 -fPIC $CFLAGS" \
+    LDFLAGS="$EM_FLAGS -O2 -s ERROR_ON_UNDEFINED_SYMBOLS=0 $LDFLAGS --relocatable"
+
+
+git clone https://github.com/google/skia.git
+cd skia
+VERSION=m93
+git checkout origin/chrome/${VERSION}
+python3 tools/git-sync-deps
+cd modules/canvaskit/
+sed -i 's/-s LLD_REPORT_UNDEFINED//g' compile.sh
+make release -j4

deps/gw.desktop

@@ -1,6 +1,6 @@
 [Desktop Entry]
 Encoding=UTF-8
-Version=0.9.3
+Version=0.10.0
 Type=Application
 Terminal=true
 Exec=bash -c "/usr/bin/gw"

docs/docs/install/Linux.md

@@ -11,7 +11,7 @@ For best performance, install GW as a desktop application on (Intel debian syste
 Use the installer below, or head over to the GitHub [Releases page](https://github.com/kcleal/gw/releases).
 
 
-[GW Intel x86_64 debian installer](https://github.com/kcleal/gw/releases/download/v0.9.3/gw_0.9.3_amd64.deb)
+[GW Intel x86_64 debian installer](https://github.com/kcleal/gw/releases/download/v0.10.0/gw_0.10.0_amd64.deb)
 
 
 

docs/docs/install/MacOS.md

@@ -11,7 +11,7 @@ For best performance, install GW as a desktop application (Intel or Apple silico
 installers below, or head over to the GitHub [Releases page](https://github.com/kcleal/gw/releases).
 
 
-[GW Intel x86_64 mac dmg installer](https://github.com/kcleal/gw/releases/download/v0.9.3/gw_macos_intel.dmg)
+[GW Intel x86_64 mac dmg installer](https://github.com/kcleal/gw/releases/download/v0.10.0/gw_macos_intel.dmg)
 
 [GW Apple arm64 mac dmg installer](https://github.com/kcleal/gw/releases/download/v0.9.3/gw-macos-arm.dmg)
 

docs/docs/install/Windows.md

@@ -25,7 +25,7 @@ Follow the installation instructions on the website to set up MSYS2 on your Wind
 Download the GW installer script below:
 
 
-[GW Intel x86_64 Windows installer](https://github.com/kcleal/gw/releases/download/v0.9.3/gw-windows-installer.vbs)
+[GW Intel x86_64 Windows installer](https://github.com/kcleal/gw/releases/download/v0.10.0/gw-windows-installer.vbs)
 
 
 Run the downloaded visual-basic script by double-clicking, or right-clicking and selecting Run as program.