Bandage v0.9.0

This is just a small update to Bandage, mainly to ensure compatibility with modern Macs but also with a few bug fixes. See the 2022 update on the README for more info about the status of Bandage development.

Changes since the previous release:

• Built to work with Qt 5.15 and Qt 6.2.
• Runs natively on Apple Silicon Macs.
• Fixed display issues with dark mode.
• Added support for SKESA fasta files.
• Fixed --colour blastrainbow with bandage image (#74).
• Added version number to the Mac app bundle (#76).
• Fixed bug with incorrect orphaned node size with bandage info (#90).
• Added custom as a colour option for command line usages (#96).

Pre-built versions included in this release:

• Mac: v11 (Big Sur) or later
  • Bandage_macOS-aarch64_v0.9.0.zip: for newer Apple Silicon Macs
  • Bandage_macOS-x86-64_v0.9.0.zip: for older Intel Macs
  • Simply download, unzip and move Bandage.app to your Applications directory.
  • If you get a 'Bandage is damaged and can't be opened' message, try running this command on the app bundle to clear the quarantine flag: xattr -cr Bandage.app
• Ubuntu: 18.04 or later
  • Bandage_Ubuntu-x86-64_v0.9.0_AppImage.zip contains an AppImage built using linuxdeployqt. This seems to be the simplest and most reliable way of running Bandage (just a single executable file) and is therefore what I'd recommend for most users.
  • Bandage_Ubuntu-x86-64_v0.9.0_AppDir.zip contains an AppDir built using linuxdeployqt. This contains all of the separate files which make up Bandage (e.g. the executable and the shared libraries).

If none of these pre-built versions work, you can try building from source or use a build from the previous release (which isn't that different).

Bandage v0.8.1

Binaries:

• The Mac app bundle should work on OS X 10.8 and later versions.
• The Windows executables should work on Windows 7 and later versions.
• Linux executables were built on two distributions: Ubuntu 14.04 and CentOS 6.7. Try whichever is more closely related to your distribution. They are also available with the Qt GUI libraries dynamically linked and statically linked. The dynamic versions provide a more native GUI experience but require the Qt5 libraries. The static versions do not require the Qt5 libraries and have fewer dependencies.

New features:

• Improved support for Canu
• Support for Unicycler graphs
• New layout type: linear layout (appropriate for reference genome graphs and plain FASTA files)
• New layout option: component separation
• Improved graph layout component packing

Bug fixes:

• Performance fixes for large BLAST searches
• Fix crash when BLAST searching for a query with no hits

Bandage v0.8.0

Binaries:

• The Mac app bundle should work on OS X 10.8 and later versions.
• The Windows executables should work on Windows 7 and later versions.
• Linux executables were built on two distributions: Ubuntu 14.04 and CentOS 6.7. Try whichever is more closely related to your distribution. They are also available with the Qt GUI libraries dynamically linked and statically linked. The dynamic versions provide a more native GUI experience but require the Qt5 libraries. The static versions do not require the Qt5 libraries and have fewer dependencies.

New features:

• Label text dynamically scales with the zoom level, reducing the need to manually change font size.
• A new command line tool, Bandage reduce, which provides a GUI-free method of saving smaller subsets of larger graphs.
• A new command line tool, Bandage info, which displays statistics about a graph file. A 'More info' button in the GUI provides the same information.
• Improved GFA support. GFA files can be loaded which do not directly include their sequences (instead using a *). If they instead keep their sequences in a separate FASTA file of the same name (as is done in ABySS), Bandage will load the sequences from the FASTA when are needed (thanks, Shaun Jackman).
• Support for ASQG graphs (used by SGA and StriDe)
• Custom colours and labels are included in saved GFA graphs and will be applied when loaded.
• When loading a CSV of graph labels, a column named 'Color' or 'Colour' will be used to set custom node colours (thanks, Tyler Barnum).

Bug fixes:

• Fix issue on Mac which could cause a crash when double-clicking the app bundle (but not when launching from the command line).
• Fix issue where BLAST queries ending in a semicolon didn't work.
• Better handling of nucleotide BLAST queries that contain N characters.
• Tolerate node depths of zero or negative depths.
• Fix overflow bug which could lead to incorrect node lengths.

Other changes:

• The OGDF code for graph layout is now included in the Bandage repository, simplifying the build procedure.
• Better zoom level limits.
• Refined command line help formatting.
• Changed 'Read depth' to 'Depth' in Bandage GUI - more general and hopefully less confusing (thanks, Israel O. Dilán).

Bandage v0.7.1

Binaries:

• The Mac version was built on OS X 10.7 and should work on all later versions as well.
• The Windows version should work on Windows 7 and later.
• Linux versions were built on two OSs: Ubuntu 14.04 and CentOS 6.7. Try whichever is more closely related to your Linux distribution. They are also available with the Qt GUI libraries statically-linked and dynamically-linked. The dynamically-linked versions may provide a more native GUI experience, but will require the installation of Qt5 libraries. The statically-linked versions do not require Qt5 libraries and have fewer dependencies.

New features:

• Can load plain FASTA files
• New querypaths command line tool to output BLAST queries without the GUI

Bug fixes:

• Command line functions which do not require the GUI no longer require the X Window System.
• Removed unnecessary characters from the start of Trinity node names (thanks, Farbod Emami!)
• Fix code to compile on CentOS
• Add support for GFA files with missing sequences
• Fix behaviour when rotating the view via Ctrl-right click dragging over a node
• Fix path sequence extraction for single circular nodes
• Fix bug with BLAST hit query coverage filter

Bandage v0.7.0

Features:

• Graph editing functionality: delete nodes/edges, duplicate nodes and merge nodes
• Manually set node names and node read depths
• Save graphs to GFA files
• Support SPAdes 3.6.1 assembly graphs

Bug fixes:

• Fixed issue preventing BLAST searches from working in Trinity graphs

Bandage v0.6.4

Features:

• Load CSV data to display on graph (thanks, Elmar Pruesse!)
• BLAST hit filters to refine searches
• Web BLAST sequences directly from Bandage
• New graph scope: Read depth range
• Show mean read depth for selected nodes
• Two-finger gesture controls for supported trackpads

Bug fixes:

• Fix unit test data directory
• Change web link to online Bandage help
• Improve support of data types in scientific notation
• Fix bug prevent BLAST functionality on Trinity graphs

Bandage v0.6.3

Features:

• Individual BLAST queries can be shown/hidden on the graph
• BLAST query table and BLAST hits table can be sorted by column
• Now possible to copy from BLAST tables
• New dialog showing details of BLAST query paths
• Filtering BLAST query paths
• Better highlighting of paths on graph
• Highlighting of BLAST query paths on graph
• BLAST error messages are more informative

Bug fixes:

• Fix issue with copying text from the GUI
• Fix GUI tab order
• Fix BLAST table column sizing

Bandage v0.6.2

Features:

• Ability to copy/save paths from the graph
• BLAST searches find graph paths to match queries
• Automatically determine node overlap for FASTG files

Bug fixes:

• Fix issue with deletion of temporary directory

Bandage v0.6.1

Features:

• tblastn is used to allow for protein queries.
• Now possible to view all BLAST searches on the graph simultaneously.
• BLAST queries are assigned colours which can be seen on the graph using the new 'BLAST hits (solid)' colour scheme.
• BLAST queries can be renamed and individually deleted.
• Multiple query FASTA files can be loaded at once.
• BLAST searches now possible from the command line with the --query option.
• BLAST hits can be labelled on the graph.

Bug fixes:

• Fix issue with node lists when using 'Around nodes' graph scope.
• Prevent duplicate query names, which could cause problems.

Bandage v0.6.0

Features:

• Enhanced command line functionality:
  • Most Bandage settings can now be specified using command line options.
  • 'Bandage load' allows users to specify a graph to load and potentially draw on launch.
  • 'Bandage image' allows users to generate an image file without ever opening the Bandage GUI.
• Change node IDs from integers to strings
  • This feature is particularly useful for Trinity, where transcript/component names can now be displayed in Bandage.
  • With this feature, partial node searches are now possible, so the user can find/draw nodes with names that partially match a string.
• Allow image saving in vector-based SVG format
• Preliminary GFA support
• Simplify graph loading into a single open file dialog
• Node labels stay in view as the graph is zoomed and panned
• Additional settings for controlling random node colours

Bug fixes:

• Fix issue with rotated labels when saving entire scene to an image file
• Improve quality of text outlines
• Expand scene boundary when nodes are dragged outside