Merge branch 'gw_dev' into master

.github/workflows/main.yml

@@ -5,7 +5,7 @@ on:
   pull_request:
 
 env:
-  version: 0.10.1
+  version: 1.0.0
 
 jobs:
   mingw:
@@ -35,75 +35,104 @@ jobs:
          name: mingw-${{ matrix.sys }}
          path: ${{ github.workspace }}/*.exe
 
-  macos-intel:
-    runs-on: macos-12
+  macos-package:
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ macos-14 ]  # macos-12,
+        include:
+          - os: macos-12
+            arch: intel
+          - os: macos-14
+            arch: m1
+
     steps:
       - uses: actions/checkout@v3
+
       - name: Install dependencies
         run: |
-          brew install graphicsmagick dylibbundler glfw fontconfig
+          brew install imagemagick graphicsmagick dylibbundler glfw fontconfig
           # npm broken for python3.12 so use this as work around
           brew list | grep python@
           # brew unlink [email protected]
           shopt -s expand_aliases
           alias python=$(brew --prefix)/bin/python3.11
           alias python3=$(brew --prefix)/bin/python3.11
-
+          
           sudo rm -rf /Library/Frameworks/Python.framework/Versions/3.12
           sudo rm -f /usr/local/bin/python3
           sudo rm -f /Library/Frameworks/Python.framework/Versions/Current/bin/python
-
+          
           which python && python --version
           which python3 && python --version
           python -m pip install packaging
           python3 -m pip install packaging
-
+          
           npm install --global create-dmg
 
-      - name: package
+      - name: Build and install htslib with libdeflate
         run: |
-          make prep
-
-          osacompile -o gw.app deps/gw_applescript_prog.txt
-          cp deps/gw_droplet.icns gw.app/Contents/Resources/droplet.icns
-
+          
+          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-* htslib && rm htslib.tar.bz2
+          
           git clone --depth 1 https://github.com/ebiggers/libdeflate.git
           cd libdeflate && CFLAGS+=' -fPIC -O3 ' cmake -B build && CFLAGS+=' -fPIC -O3 ' cmake --build build
-          cp build/libdeflate.a /usr/local/lib && cp libdeflate.h /usr/local/include && cd ../
+          cp build/libdeflate.a ../htslib
+          cp libdeflate.h ../htslib
+          ls ../htslib
 
-          wget -O htslib.tar.bz2 https://github.com/samtools/htslib/releases/download/1.18/htslib-1.18.tar.bz2
-          tar -xvf htslib.tar.bz2 && mv htslib-* htslib && rm htslib.tar.bz2 && cd htslib
-          ./configure --enable-libcurl --enable-s3 --enable-lzma --enable-bz2 --with-libdeflate
-          make && make install && cd ../
+          cd ../htslib
+          LDFLAGS="$LDFLAGS -L./" CPPFLAGS="$CPPFLAGS -I./" ./configure --enable-libcurl --enable-s3 --enable-lzma --enable-bz2 --with-libdeflate
+          make
+          sudo make install
 
+      - name: Make Prep
+        run: |
+          make prep
+
+      - name: package
+        run: |
+          
+          osacompile -o gw.app deps/gw_applescript_prog.txt
+          cp deps/gw_droplet.icns gw.app/Contents/Resources/droplet.icns
+          
           echo "BUILDING GW"
-          make
+          
+          brew_lib=$(brew --prefix)/lib
+          brew_include=$(brew --prefix)/include
+          brew_bin=$(brew --prefix)/bin
+          
+          LDFLAGS="${LDFLAGS} -L${brew_lib}" CPPFLAGS="${CPPFLAGS} -I${brew_include}" make
+          
           mv gw ./gw.app/Contents/MacOS
           rm -rf include lib src Makefile
-
-          dylibbundler -od -b -x ./gw.app/Contents/MacOS/gw -d ./gw.app/Contents/libs/ -p @executable_path/../libs/
-
+          
+          PATH="$PATH:$brew_bin" dylibbundler -od -b -x ./gw.app/Contents/MacOS/gw -d ./gw.app/Contents/libs/ -p @executable_path/../libs/
+          
           echo "VALIDATION"
           otool -L gw.app/Contents/MacOS/gw
           echo ""
-
+          
           echo "CODE SIGNING"
           ls -l
           sudo chown -R $(whoami) ./gw.app
           chmod -R a+rw ./gw.app
-          codesign --remove-signature ./gw.app
-          codesign --force --deep -s - gw.app -v
-          codesign --verify -vvvv gw.app
-          create-dmg 'gw.app' || true
+          sudo codesign --remove-signature ./gw.app
+          sudo codesign --force --deep -s - gw.app -v
+          sudo codesign --verify -vvvv gw.app
+          
+          PATH="$PATH:$brew_bin" create-dmg 'gw.app' || true
           ls
-          mv gw\ undefined.dmg gw_macos_intel.dmg
+          mv gw\ undefined.dmg gw_macos_${{ matrix.arch }}.dmg
           ls
           pwd
 
       - name: upload
         uses: actions/upload-artifact@v3
         with:
-          name: gw_macos_intel
+          name: gw_macos_${{ matrix.arch }}
           path: ./*.dmg
 
   deb-package:
@@ -115,31 +144,31 @@ jobs:
           sudo apt update
           sudo apt-get install dh-make build-essential debhelper dh-virtualenv
           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 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
         run: |
-          
+
           BUILD_DIR=$(pwd)
-          
+
           mkdir -p usr/bin
           mkdir -p usr/lib/x86_64-linux-gnu
           mkdir -p usr/lib/gwhts
           mkdir -p usr/include/gwhts
           mkdir -p usr/share/icons
           mkdir -p usr/share/icons/hicolor/512x512/apps/
           mkdir -p usr/share/applications
-          
+
           sudo mkdir -p /usr/lib/gwhts
           sudo mkdir -p /usr/include/gwhts/htslib
           sudo cp /usr/lib/x86_64-linux-gnu/libglfw* usr/lib/x86_64-linux-gnu/.
-          
+
           git clone --depth 1 https://github.com/ebiggers/libdeflate.git
           cd libdeflate && CFLAGS+=' -fPIC -O3 ' cmake -B build && CFLAGS+=' -fPIC -O3 ' cmake --build build
           sudo cp build/libdeflate.a /usr/local/lib && sudo cp libdeflate.h /usr/local/include
           echo "LIBDEFLATE BUILT" && pwd
           cd ${BUILD_DIR}
-          
+
           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-1.20 htslib && rm htslib.tar.bz2 && cd htslib
@@ -148,39 +177,39 @@ jobs:
           make -j3
           echo "HTSLIB BUILT" && pwd
           cp -rf htslib ../include
-          sudo cp libhts.* /usr/lib/gwhts 
+          sudo cp libhts.* /usr/lib/gwhts
           sudo cp htslib/*.h /usr/include/gwhts/htslib
           cp libhts.* ${BUILD_DIR}/usr/lib/gwhts
-          
+
           cd ${BUILD_DIR}
-          
+
           sed -i '133 i \\t-mv gw usr/bin' Makefile
           sed -i 's@-L/usr/local/lib@-L/usr/local/lib -L/usr/lib/gwhts@g' Makefile
-          
+
           make prep
-          
+
           cp include/gw_icon.png usr/share/icons/
           cp include/gw_icon.png usr/share/icons/hicolor/512x512/apps/
           cp deps/gw.desktop usr/share/applications/
 
       - name: package
         run: |
           dh_make --single --createorig --packagename gw_${version} --email [email protected] --yes --native
-          
+
           printf "usr/bin/gw\nusr/share/icons/gw_icon.png\nusr/share/applications/gw.desktop\nusr/lib/gwhts/\nusr/lib/x86_64-linux-gnu/libglfw.so.3\nusr/lib/x86_64-linux-gnu/libglfw.so.3.3" > debian/install
-          
+
           export LDFLAGS="$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
-          
+
           # 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 -us -uc
 
       - name: upload

.gitignore

@@ -39,4 +39,5 @@ libgw.so
 /gw.wasm
 /wasm_libs
 /src/plot_commands.o
+/src/ideogram.o
 /.gw_session.ini

.gw.ini

@@ -28,6 +28,7 @@ ylim=50
 coverage=true
 log2_cov=false
 expand_tracks=true
+scale_bar=true
 link=none
 scale_bar=true
 split_view_size=10000
@@ -40,13 +41,13 @@ font_size=14
 sv_arcs=true
 mods=false
 mods_qual_threshold=50
-session_file=
+session_file=/Users/sbi8kc2/CLionProjects/gw/.gw_session.ini
 
 [view_thresholds]
 soft_clip=20000
 small_indel=100000
 snp=500000
-mod=250000
+mod= 1000000
 edge_highlights=1000000
 variant_distance=100000
 low_memory=1500000
@@ -61,7 +62,6 @@ scroll_up=PAGE_UP
 
 [interaction]
 cycle_link_mode=L
-print_screen=PRINT_SCREEN
 find_alignments=F
 repeat_command=R
 vcf_as_tracks=false
@@ -71,11 +71,9 @@ bed_as_tracks=true
 number=3x3
 parse_label=filter
 labels=PASS,FAIL
-delete_labels=DELETE
-enter_interactive_mode=ENTER
 
 [shift_keymap]
-ampersand=7
+ampersand= 7
 bar=\
 colon=;
 curly_open=[

README.rst

@@ -15,7 +15,7 @@ GW
 .. |Dl badge| image:: https://img.shields.io/conda/dn/bioconda/gw.svg
    :target: http://bioconda.github.io/recipes/gw/README.html
 
-.. image:: include/banner.png
+.. image:: include/resources/images/banner.png
     :align: center
 
 
@@ -102,7 +102,7 @@ To view a genomic region e.g. chr1:1-20000, supply an indexed reference genome a
 
     gw hg38 -b your.bam -r chr1:1-20000
 
-.. image:: include/chr1.png
+.. image:: include/resources/images/chr1.png
     :align: center
 
 
@@ -112,7 +112,7 @@ A variant file in .vcf/.bcf format can be opened in a GW window by either draggi
 
     gw hg38.fa -b your.bam -v variants.vcf
 
-.. image:: include/tiles.png
+.. image:: include/resources/images/tiles.png
     :align: center
 
 

deps/gw.desktop

@@ -1,6 +1,6 @@
 [Desktop Entry]
 Encoding=UTF-8
-Version=0.10.1
+Version=1.0.0
 Type=Application
 Terminal=true
 Exec=bash -c "/usr/bin/gw"

docs/Gemfile

@@ -3,7 +3,7 @@ source 'https://rubygems.org'
 gem "jekyll", "~> 4.3.2" # installed by `gem jekyll`
 # gem "webrick"        # required when using Ruby >= 3 and Jekyll <= 4.2.2
 
-gem "just-the-docs", "0.5.4" # pinned to the current release
+gem "just-the-docs", "0.8.2" # pinned to the current release
 # gem "just-the-docs"        # always download the latest release
 
 # gem "github-pages", group: :jekyll_plugins

docs/Gemfile.lock

@@ -58,7 +58,7 @@ GEM
     rb-fsevent (0.11.2)
     rb-inotify (0.10.1)
       ffi (~> 1.0)
-    rexml (3.2.5)
+    rexml (3.2.7)
     rouge (3.30.0)
     safe_yaml (1.0.5)
     sass-embedded (1.58.3)

docs/docs/guide/Alignments.md

@@ -2,7 +2,7 @@
 title: Alignment data
 layout: home
 parent: User guide
-nav_order: 1
+nav_order: 3
 ---
 
 # Alignment data
@@ -11,18 +11,29 @@ The easiest way to load an alignment file (bam or cram format) is to start
 GW and drag-and-drop a file into the window. This will open the file and navigate
 to the first chromosome in the bam file header, showing the first 20 kb.
 
-Using the CLI the same can be achieved using:
+You can also use the `load` command from inside GW. Typing `load` in the command box followed
+by the path to your bam file (not you can use tab-completion when using this command):
+
+```
+load ~/Desktop/your.bam
+```
+
+Navigate to a new region by typing e.g. `chr2` into the command box, or add a new region using `add chr2`
+
+Using the CLI, bam files are loaded using:
 
 ```shell
 gw hg38 -b your.bam -r chr1:1-20000
 ```
 
+
 ![Alt text](/assets/images/ui2.png "GW")
 
 The hg38 argument is a genome-tag listed in the config file and will load a remote reference genome.
 
 For much faster performance, either replace the argument with the path to a local file,
-or change the config file to point to a local file rather than a remote reference genome.
+or change the config file to point to a local file rather than a remote reference genome (see Genomes section
+for more detail).
 This command will open a GW window that can be used interactively with the mouse and keyboard.
 Note multiple -b and -r options can be used.