./biology/py-cutadapt, Find and remove adapter sequences, primers, poly-A tails, etc

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Branch: CURRENT, Version: 4.7, Package name: py312-cutadapt-4.7, Maintainer: pkgsrc-users

Cutadapt finds and removes adapter sequences, primers, poly-A tails
and other types of unwanted sequence from your high-throughput
sequencing reads.

Master sites:

Filesize: 245.013 KB

Version history: (Expand)

CVS history: (Expand)


   2024-04-11 01:47:55 by Jason Bacon | Files touched by this commit (1) 
Log message:
biology/py-cutadapt: Release to pkgsrc-users@

Cutadapt has been replaced by fastq-trim in my toolbox
   2024-03-20 23:29:39 by Jason Bacon | Files touched by this commit (1) 
Log message:
biology/py-cutadapt: Restore setuptools and setuptools_scm

Builds without them listed as deps if they happen to be installed,
but fails on a blank pkgsrc installation
   2024-03-16 14:46:42 by Jason Bacon | Files touched by this commit (3) | Package updated
Log message:
py-cutadapt: Update to 4.7 (minor update)

Send error message to stderr
Add support for single-ended uBAM
Drop Python 3.7

Changes: https://cutadapt.readthedocs.io/en/stable/changes.html
   2024-02-18 12:14:08 by Thomas Klausner | Files touched by this commit (1) 
Log message:
py-cutadapt: add missing tool

Remove egg.mk leftover.
   2024-02-10 14:12:35 by Jason Bacon | Files touched by this commit (5) 
Log message:
biology/py-cutadapt: Update to 4.6

Numerous bug fixes and enhancements since 3.5
Changes: https://github.com/marcelm/cutadapt/tags

Also replaced ALTERNATIVES with PYTHON_SELF_CONFLICT
ALTERNATIVES does not work automatically and there is no reason
to have more than one installation of py-cutadapt
   2022-11-17 00:02:14 by Thomas Klausner | Files touched by this commit (1) 
Log message:
py-cutadapt: fix build with python 3.11
   2022-01-17 10:03:10 by Adam Ciarcinski | Files touched by this commit (3) | Package updated
Log message:
py-cutadapt: updated to 3.5

v3.5 (2021-09-29)
-----------------

* :issue:`555`: Add support for dumping statistics in JSON format using ``--json``.
* :issue:`541`: Add a "Read fate breakdown" section heading to the \ 
report, and also
  add statistics for reads discarded because of ``--discard-untrimmed`` and
  ``--discard-trimmed``. With this, the numbers in that section should add up to \ 
100%.
* Add option ``-Q``, which allows to specify a quality-trimming threshold for R2 \ 
that is
  different from the one for R1.
* :issue:`567`: Add ``noindels`` adapter-trimming parameter. You can now write
  ``-a "ADAPTER;noindels"`` to disallow indels for a single adapter only.
* :issue:`570`: Fix ``--pair-adapters`` not finding some pairs when reads contain
  more than one adapter.
* :issue:`524`: Fix a memory leak when using ``--info-file`` with multiple cores.
* :issue:`559`: Fix adjacent base statistics not being shown for linked adapters.
   2022-01-05 16:41:32 by Thomas Klausner | Files touched by this commit (289) 
Log message:
python: egg.mk: add USE_PKG_RESOURCES flag

This flag should be set for packages that import pkg_resources
and thus need setuptools after the build step.

Set this flag for packages that need it and bump PKGREVISION.