GraphMap v0.3.0

Many important updates compared to previous version, including:

• change in command line arguments - the current version is not compatible to the previous ones, please read the usage details
• precompiling of the libraries is no longer required - simply make modules and the codebase will be synced and ready for compilation with the main code.
• reorganized major parts of the code
• new output format: BLASR's m5
• set default thresholds on the E-value and the mapq
• ...and much more.

For more details, check out the changelog.

Patch for anchored mode alignment

There were two subtile bugs with the anchored alignment which would be observed mostly only when aligning over large N regions.

Overlapping modes + bug fixes

In this version overlap modes ('-w owler' and '-w overlapper' are merged from the dev branch. Also, many tiny bug fixes have been made from release 0.21, as well as an increase in speed of processing, especially for Illumina-type data.

GraphMap preprint version

This version of the GraphMap algorithm was used for the purposes of our preprint manuscript.