GFAKluge - Make fix

Attempts to fix an issue with tabs/spaces in the makefile that break the build.

Scientific Software - Peer-reviewed - C++
Published by edawson about 5 years ago

GFAKluge - 1.1.2

This contains some minor changes from the review process:

• [X] make examples.md a link to that file
  
• [X] set the GitHub website link to the appropriate documentation (now links to README / GitHub Pages)
  
• [X] make interface.md a link to that file
  
• [X] bash-tap/bash-tap-bootstrap be included in the source code (made bash-tap) a git submodule, meaning it's now downloaded with git clone --recursive
  
• [X] You may want to consider using Autotools (I'm going to run through some tutorials and see if I can incorporate this - thanks for the suggestion!)
• [X] make install installs pliib.hpp and tinyfa.hpp
• [X] bump version to 1.1.2
• [X] fix make install instructions

Scientific Software - Peer-reviewed - C++
Published by edawson about 7 years ago

GFAKluge - Paper release

This release brings the changes requested by @sjackman in the JOSS review.

[X] Fix install instructions [X] Remove citation to repo in summary [X] Mention the homepage and license in the summary [X] Make GFAKluge a header-only library [X] Add a make install target to makefile [X] Change the wording of "legacy GFA formats" [X] Reference GFApy and RGFA and ABYSS, all of which are other programs which can convert GFA 1 -> 2 [X] Fix typesetting of convert [X] Fix typesetting of vg msga [X] Change wording to reflect that GFA2 and GFA1 interconversion needs are not temporary [X] List the currently available commands in the manuscript. [X] Give command line examples of three or more commands [X] Mention the API documentation in the manuscript [X] Add a make test target in the makefile that runs automated tests [X] Add a contributing section to the Readme

Scientific Software - Peer-reviewed - C++
Published by edawson about 7 years ago

GFAKluge - Version 1.0

This release has a bunch of bug fixes and contains all the basic functionality we desired for submission.

Scientific Software - Peer-reviewed - C++
Published by edawson over 7 years ago

GFAKluge -

Fixes a bug where fillseq output was not deterministic. Should also fix a nasty quadratic runtime issue when reading paths and another where reading path lines sometimes crashed due to weird pointer weather.

Scientific Software - Peer-reviewed - C++
Published by edawson over 7 years ago

GFAKluge - 0.3.0

This release deprecates the walkelem and instead support GFA0.1 using the pathelem as the backing container. It also adds the fillseq command. There are bug fixes related to segment orientations in paths and a performance improvement in path normalization.

Scientific Software - Peer-reviewed - C++
Published by edawson over 7 years ago

GFAKluge - Streaming output

This release adds a few new features: - streaming output by calling write_element(<element>) - FASTA formatted output in the convert too

It also refactors the pliib.hpp file to reside in the repo, rather than as a submodule.

Scientific Software - Peer-reviewed - C++
Published by edawson almost 8 years ago

GFAKluge - Swap version and spec flags, switch split functions, Bug fixes

This is a minor tweak to 0.2.0 that swaps the --version <X> flag to the more GNU-esque behavior of printing the software version when the --version flag is passed (NB: no argument). The GFA output version can be controlled using the --spec <X> flag.

This also swaps the gfakluge::split function for the pliib::split function, which should make swapping out to the zero-copy version easier.

A bug which caused a segfault when sorting GFA2 and outputting GFA1 was fixed.

Scientific Software - Peer-reviewed - C++
Published by edawson almost 8 years ago

GFAKluge - GFA Harmony

This release brings full compatibility with GFA0.1, GFA1.0, and the GFA1.0 compatible subset of GFA2.0.

• Executable is now named gfak, not "gfakluge"
• New --version <X> flag for relevant tools that allows users to select which format to use for output.
• gfak extract: create a fasta file from the S lines of a GFA file.
• No information is lost in the backing containers when switching between formats, though incompatible records are removed from output.
• Crushed a few bugs (an off by one error, some segfaults, etc)
• Several helpful changes/fixes from other devs (namespace rules, output bug fix)

Scientific Software - Peer-reviewed - C++
Published by edawson almost 8 years ago

GFAKluge - GFA 0.1 <-> 1.0

This release supports all of the variants of GFA 0.1 / 1.0 I have thus far observed. I'm pushing it out now in preparation for the forthcoming merge of the dev branch that brings full GFA2 compatibility.

Scientific Software - Peer-reviewed - C++
Published by edawson over 8 years ago