v0.21

Mash files (.msh) can now be used as input.

v0.20

v0.20

v0.16

• Removed Thread::Queue in favor of arrays. Hopefully not locking other threads will make large-threaded runs run faster (e.g., --numcpus 100). It seems to trim off a second on some trial runs, so it is might be doing the job but not necessarily a huge decrease.
• --version is easier to parse from other programs
• Fixed random bugs having to do with .gbk.gz inputs
• v0.15 is on CPAN and is almost the same as this version except --version

v0.14

• Optimized adding distance to the database some more. Seems to have shaved off half a second on my 85-genome assemblies test set with 32 or 64 threads.
• Added --version. It is also shown in the documentation but not yet in README.md.
• Made compatible with CPAN and Travis CI. This includes unit tests. So far v0.12 is in CPAN.
• Checking for files of the same basename in case multiple input directories are involved.

v0.12 - with unit testing

• Conforms better to the standard Perl project format
  • The user is now responsible for installing bioperl and any other perl modules
  • t/ directory with test data now present
  • make test instead of make check
• I figured out how to use travis-ci for unit testing. Ready for any pull requests!
• Minor changes to README.md

v0.11 - richseq and compressed files now welcome

• Richseq files - gbk, embl, and swissprot are now accepted
• Compressed files - .gz, .bz2, and .zip are now accepted.

These changes have not been tested, hence the pre-release tag.

v0.10

• GenBank, EMBL, and SwissProt support for genome assemblies
• Extra cpus are not wasted as much: Mash will be run with multiple threads if extra cpus are given with --numcpus.
• Refactored the minimum abundance filter and added KMC support. However, KMC does not seem to be as accurate for detecting peaks and valleys in kmer frequencies.

v0.09

• Fixed the minimum abundance filter bug where it was not triggered with a depth of 0
• Added onto the Makefile for checking prerequisite software
• Output distance matrix is now a well-defined flag in both mashtree.pl and mashtree_wrapper.pl instead of a hidden feature
• Updated documentation

v0.08 - the database edition

• SQLite added
• Readme.md and Makefile reflect new SQLite addition
• SQLite is a prerequisite now
• Multithreaded mashtree_wrapper.pl

v0.07

• more multithreading
• jellyfish is used if present for the minimum abundance filter, if it's present