export: fixed a bug where exporting to tab format with a header would not export the first line of data

grep: fixed --id-list option

import: can now import SILVA fasta files, and now handling sequences with Uracil (U) nucleotides (by converting them to Thymine (T) for now)

addtaxids: new command to annotate sequences with their NCBI taxid based on their taxon name

obi ls: reworked a bit (mostly just now done in C instead of Cython)

ecotag: added separate threshold for minimum circle identity (sequence is assigned to the LCA of all sequences within a similarity circle of the best matches; the threshold for this circle is the highest value between the chosen minimum circle identity and the best assignment score found)

obi cat: fixed open file descriptor leak

obi cat: fixed a bug introduced in 3.0.0b28 (KeyError: 'noprogressbar')

• export: now automatically sorts dictionary keys alphabetically for tab/csv output
• various small bug fixes and improvements

• export: fixed a bug introduced in version v3.0.0b28
• ls: added more information about view creation date and OBITools3 version

• alignpairedend: fixed division by 0 error introduced in version v3.0.0b28

• import: added --space-priority option to prioritize saving space over time when importing a view with a line selection associated

• fixed and improved the associated column system

• all commands: now handle output to buffer object (e.g. stdout)
• ngsfilter: unidentified sequences are now kept untrimmed
• alignpairedend: improved/fixed the output tags for the alignment score and lengths
• grep: now prints the number of entries grepped

• uniq: Fixed a bug where some sequences were not properly dereplicated
• clean: Fixed the behaviour when no or bad sample information is given

• export: dictionaries are now formatted as they were in the original OBITools, and fixed tuple formatting

• ngsfilter: reversed tag is now set to 'False' instead of 'None' when false.

• ngsfilter: made one of the tag error messages more accurate
• grep and uniq now output empty views when the input is an empty view
• ls: fixed an issue with big DMS

• Improved ecotag output with list of taxids of best matches
• Improved uniq progress bar
• Fixed bash history display for views
• Fixed bugs with the output of sequences unaligned ('joined') by alignpairedend
• Fixed a bug where tuple columns would 'lose' their indexer in some cases

Fixed installation on Ubuntu without pip.

Fixed a bug when skipping unreadable sequences in obi import

Improved import of Genbank files

Reworked installation for pip + minor fixes