Gfakluge Versions Save

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

This contains some minor changes from the review process:

• make examples.md a link to that file
• set the GitHub website link to the appropriate documentation (now links to README / GitHub Pages)
• make interface.md a link to that file
• 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
• 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!)
• make install installs pliib.hpp and tinyfa.hpp
• bump version to 1.1.2
• fix make install instructions

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

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

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.

This release deprecates the walk_elem and instead support GFA0.1 using the path_elem 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.

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.

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.

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)

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.