v2.3.3

What's Changed

• in util.version.py::get_project_path(), consider calling modules to report VERSION correctly by @tomkinsc in #109

Full Changelog: v2.3.2...v2.3.3

v2.3.2

What's Changed

functionality updates

• In cmd.py argparse common_args(), set default number of threads to all available if --threads is unspecified by @tomkinsc in #104
• index bam before calling samtools idxstats; warn user if input lacks reads by @tomkinsc in #102

dependency updates

• add fgbio to conda dependencies by @tomkinsc in #103
• update viral-baseimage 0.2.2 -> 0.2.3 (with fully-featured qsv) by @tomkinsc in #100

build updates

• update coverage config and testing config inherited by derived docker images by @tomkinsc in #99
• fix docbuild by @dpark01 in #106
• more ReadTheDocs fixes by @dpark01 in #107

Full Changelog: v2.3.1...v2.3.2

v2.3.1

• Update docker base image from viral-baseimage 0.2.1 -> 0.2.2 (PR #97)
• Update python version 3.8 -> 3.10, and also associated dependencies necessary for py 3.10 (PR #98)

v2.3.0

• This adds a new CLI function, read_utils.py::filter_bam_to_proper_primary_mapped_reads() to remove from a bam file any reads not flagged as being properly paired. This same functionality is also now available as an optional post-alignment operation of minimap2_idxstats and bwamem_idxstats if --filterReadsAfterAlignment is specified.

v2.2.4

• add firecloud python library (for Terra) to conda-installed python dependencies
  • Note: this library is anticipated to be superseded by a new Terra API library in the future

v2.2.3

Changes related to unit+integration testing:

• Update pytest 5.4.3 -> 7.4.3
• Update conftest.py to account for breaking changes in the newer version of pytest

v2.2.2

The package jq is now available on the PATH.

v2.2.1

• bump pysam min pin to >=0.20.0
• bump samtools min pin >=1.16.1

v2.2.0

• update viral-baseimage to 2.2.0, bearing underlying OS upgrade from Ubuntu 18.04 LTS (bionic) to Ubuntu 22.04 LTS (jammy)
• build fixes for documentation (dependency changes) to fix local builds and builds on ReadTheDocs
• migration from Travis CI to GitHub Actions for testing and docker image deployment to quay.io

v2.1.33

• push R fix into docker image [#77]
• add median and mean options to binning stat for plot_coverage [#76]