Cutadapt

Latest version: v4.7

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4.7

-----------------

* :issue:`767`: Error messages are always sent to stderr. They were
previously sent to stdout when using `-o`.
* Cutadapt can now read single-end data from unaligned BAM files (uBAM).
* Dropped support for Python 3.7.

4.6

-------------------

* :issue:`744`, :issue:`561`: Make ``--revcomp`` work with paired-end data.

4.5

-----------------

* :pr:`725`: Added a ``--max-average-error-rate``/``--max-aer`` option to add a filter
that checks if the number of expected errors divided by read length is above a
certain threshold. The expected errors are calculated the same as in
``--max-expected-errors``, and dividing by read length helps for reads that
have varying lengths.
* :issue:`696`: Added a histogram of the lengths of removed poly-A tails to
the report.
* :issue:`696`: For paired-end data, ``--poly-a`` was changed to trim poly-T
"heads" on R2 (this is still experimental as it is unclear whether that is
the desired behavior. Please give feedback!)
* A poly-A tail is only removed if it is at least three nucleotides long.
* :issue:`734`: Fixed misassignments during demultiplexing that would sometimes
happen when there are collisions between adapter sequences
(when the warning "sequence ... cannot be assigned uniquely" was printed).
Previously, sequences could incorrectly be assigned to an adapter that is not
actually the best match.

4.4

-----------------

* :issue:`695`: Fixed very slow k-mer heuristic initialization (hours instead
of seconds) for degenerate adapter sequences such as ``A{100}`` as used
when doing poly-A trimming.
* :issue:`696`: Added option ``--poly-a`` for trimming poly-A tails. This is
more accurate and multiple times faster than using ``-a A{100}`` as previously
recommended. This is currently experimental (that is, the algorithm may change
in the next one or two releases).
* :issue:`685`: Sped up index generation somewhat. This is most noticable when
demultiplexing using thousands or more adapters. The speedup is
different depending on whether indels are allowed or not because
different algorithms are used.
* :issue:`685`: Sped up demultiplexing (when using an index) for the case when
the read contains ``N`` bases within the region where the adapter matches.
Previously, any ``N`` would disable the index for that read and trigger a
fallback to the slow method of matching each adapter one-by-one. Now the index
is used even in those cases.
* :pr:`700`: Sped up ``--max-expected-errors``. Thanks rhpvorderman.

4.3

-----------------

* :pr:`663`: Cutadapt became significantly faster due to an added runtime
heuristic that avoids running the full alignment algorithm if it can be
proven that it cannot succeed. Thanks to rhpvorderman for this great
improvement!
* :issue:`665`: 5' adapters did not allow partial matches in the beginning
when the :ref:`rightmost <rightmost>` adapter-search parameter was used.
* :issue:`662`: Fixed assertion error when ``--discard-untrimmed`` was used
together with ``--json`` and demultiplexing.
* :issue:`674`: When reading 3' adapters from an external file, they can now
all be anchored by using the syntax ``-a file$:adapters.fasta`` (note the
``$`` in ``file$:``).
* :issue:`669`: The ``--rename`` option now understands the ``\t`` escape
sequence and will insert a tab character in its place. This is useful when
transferring FASTQ header comments to SAM tags.

4.2

-----------------

* :issue:`654`: When determining the error rate for a partial match of an
adapter with ``N`` wildcards, the number of non-N bases was not computed
correctly, which could lead to matches not being found.
* :issue:`546`: Automatically replace ``I`` in adapter sequences with ``N``.
``I`` is used to encode inosine, which matches any base. Contributed by peterjc.
* :issue:`528`: Cutadapt should now no long hang in multicore mode when an error
was raised in a worker process (for example, when an incorrectly formatted
FASTQ file was encountered).

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