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v3.0.0b39
export
: fixed a bug where exporting to tab format with a header would not export the first line of data- Source code
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v3.0.0b37
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- Source code
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v3.0.0b36
obi ls
: reworked a bit (mostly just now done in C instead of Cython)- Source code
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v3.0.0b35
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)- Source code
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v3.0.0b34
obi cat
: fixed open file descriptor leak- Source code
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v3.0.0b33
obi cat
: fixed a bug introduced in 3.0.0b28 (KeyError: 'noprogressbar'
)- Source code
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v3.0.0b32
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export
: now automatically sorts dictionary keys alphabetically for tab/csv output - various small bug fixes and improvements
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v3.0.0b31
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export
: fixed a bug introduced in versionv3.0.0b28
-
ls
: added more information about view creation date and OBITools3 version
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v3.0.0b30
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alignpairedend
: fixed division by 0 error introduced in versionv3.0.0b28
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v3.0.0b29
import
: added--space-priority
option to prioritize saving space over time when importing a view with a line selection associatedfixed and improved the associated column system
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v3.0.0b28
- 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
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- all commands: now handle output to buffer object (e.g.
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v3.0.0b27
-
uniq
: Fixed a bug where some sequences were not properly dereplicated -
clean
: Fixed the behaviour when no or bad sample information is given
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v3.0.0b26
export
: dictionaries are now formatted as they were in the original OBITools, and fixed tuple formattingngsfilter
:reversed
tag is now set to 'False' instead of 'None' when false.
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v3.0.0b25
-
ngsfilter
: made one of the tag error messages more accurate -
grep
anduniq
now output empty views when the input is an empty view -
ls
: fixed an issue with big DMS
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v3.0.0b24
- 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
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- Improved
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v3.0.0b22
Fixed a bug when skipping unreadable sequences in
obi import
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