v1.5.2

Quick fixes:

• Revert fasta indexing to samtools instead of pysam (for py3 threaded stability).
• Fix up metagenomics snakemake rules.
• Clean up some Tool executions to subprocess calls (vs custom code).
• Add pycodestyle to requirements-test.txt, as it is required for mock, but not listed as a requirement by mock.

v1.5.1

Fix: the GATK wrapper is now adapted for conda-based installs of GATK. License and manual download of GATK is still required, but the gatk conda package provides the gatk-register command which can be used to copy a licensed jar file into the conda environment.

v1.5.0

Robust behavior in depletion, assembly and metagenomics for empty or almost-empty data sets. More interpretable Trinity errors. Multithreaded LASTAL filtering. Overview diagram in documentation.

v1.4.5

In the deplete stage, blastn performance has been improved: calls to blastn are parallelized via separate blastn processes on chunked input rather than by specifying multiple threads for a single blastn process. Bug fix for conda install path determination.

v1.4.4

Made the CondaPackage() install method more flexible in detecting active conda environments, particularly for older conda releases that use CONDA_DEFAULT_ENV inconsistently (env path vs env name).

v1.4.3

Packages installed via conda now look for an active conda environment as the install location before falling back to a location within the viral-ngs directory; Kraken install is now only Conda-based; lastal input files are now chunked into 100k-read batches. Internal cleanups, and some changes to automated testing.

v1.4.2

Added LCA metagenomics functions for parsing blast/diamond output. Shifted testing infrastructure to py.test from nose. More multithreaded blast improvements in human depletion steps. Improvements to command line help output.

v1.4.1

Bug fixes to tool installation.

v1.4.0

Implementation of basic metagenomics tools: kraken and krona. Bug fix for silent tool failures introduced in March 2016. Multithreaded blastn. More verbose stats in scaffolding.

v1.3.5

Tune nucmer parameters in scaffolding step to tolerate more diverse viruses (HIV, Influenza). Misc bugfixes related to version-detection, lastal, and Genbank submission scripts.