v1.0.11

• Fixed lineage_wf CLI bug causing crash due to missing coverage_file argument.

v1.0.10

• required version number update for upload to Pypi

v1.0.9

• removed ScreamingBackpack as a dependency and modified CheckM to never removes user files
• added "life" as an acceptable rank for the taxonomy_wf so the universal Prokaryotic marker set can be used
• fixed bug with processing empty gene files
• fixed bug with processing identical user genomes which cause pplacer to create polytomies

v1.0.8

• Fix for the lineage_wf command that was causing an invalid marker set to be selected in rare cases when using the reduced_tree flag. This issue was resulting in CheckM failing with "[Error] Failed to set a selected lineage-specific marker set."

v1.0.7

• fixed incorrect reporting of number of marker genes/sets for taxonomic-specific marker sets

v1.0.6

• minor bug fixes
• fixed pplacer_threads issue with the checkm test command
• fixed issue with checkm setRoot /my/data/directory interactively requesting the data directory

v1.0.5

• added --pplacer_threads flag to the tree and lineage_wf commands in order to allow control over the number of threads used by pplacer. This can substantially help with the peak memory requirements of CheckM.
• minor bug fixes

v1.0.4

Minor bug fixes and enhancements:

• removed import of pylab as this may have a GTK dependency.
• moved to pysam >= v0.8.0 for coverage calculation.
• added checks for expect sequence types (nucleotide vs. amino acid).
• fixed bug with 'tetra' command when processing lowercase bases.

v1.0.3

• fixed incompatibility with generic feature file (GFF) output for Prodigal >= v2.6.1

v1.0.2

• fixes issue with pysam that was causing the checkm coverage command to report no mapped reads