head 1.8; access; symbols pkgsrc-2023Q4:1.6.0.16 pkgsrc-2023Q4-base:1.6 pkgsrc-2023Q3:1.6.0.14 pkgsrc-2023Q3-base:1.6 pkgsrc-2023Q2:1.6.0.12 pkgsrc-2023Q2-base:1.6 pkgsrc-2023Q1:1.6.0.10 pkgsrc-2023Q1-base:1.6 pkgsrc-2022Q4:1.6.0.8 pkgsrc-2022Q4-base:1.6 pkgsrc-2022Q3:1.6.0.6 pkgsrc-2022Q3-base:1.6 pkgsrc-2022Q2:1.6.0.4 pkgsrc-2022Q2-base:1.6 pkgsrc-2022Q1:1.6.0.2 pkgsrc-2022Q1-base:1.6 pkgsrc-2021Q4:1.5.0.2 pkgsrc-2021Q4-base:1.5 pkgsrc-2021Q3:1.3.0.4 pkgsrc-2021Q3-base:1.3 pkgsrc-2021Q2:1.3.0.2 pkgsrc-2021Q2-base:1.3 pkgsrc-2021Q1:1.2.0.2 pkgsrc-2021Q1-base:1.2; locks; strict; comment @# @; 1.8 date 2024.03.16.13.46.42; author bacon; state Exp; branches; next 1.7; commitid g7vcgWauPDd3co2F; 1.7 date 2024.02.10.13.12.35; author bacon; state Exp; branches; next 1.6; commitid MedMeHQr9Bpt7TXE; 1.6 date 2022.01.17.09.03.10; author adam; state Exp; branches; next 1.5; commitid HvhkPFcgslAeZXoD; 1.5 date 2021.10.26.10.03.43; author nia; state Exp; branches; next 1.4; commitid R64ULQLy8JYkZieD; 1.4 date 2021.10.07.13.19.42; author nia; state Exp; branches; next 1.3; commitid CQ422EVgQgYxGSbD; 1.3 date 2021.03.31.09.23.56; author adam; state Exp; branches; next 1.2; commitid bsXiD4awfYThurNC; 1.2 date 2021.03.08.07.10.56; author adam; state Exp; branches; next 1.1; commitid 16acOenJ2lNtutKC; 1.1 date 2021.02.08.01.55.23; author bacon; state Exp; branches; next ; commitid fGlE9cy1f6B7EQGC; desc @@ 1.8 log @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 @ text @$NetBSD$ BLAKE2s (cutadapt-4.7.tar.gz) = f5b03c53fc169c1c9398c40ffc34de0b54a79a082df3064035c0780aef5cde8f SHA512 (cutadapt-4.7.tar.gz) = 975a12899fc014b645839ab4ebc1cbb9df7c87d4c4bef67976a72b657d7c274a49edf08e7dfa935d893cf7af35027a0cc04ceb79be0766cbe9ca49c5a2a85c61 Size (cutadapt-4.7.tar.gz) = 250893 bytes @ 1.7 log @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 @ text @d3 3 a5 3 BLAKE2s (cutadapt-4.6.tar.gz) = 5a77d2a4b39e59f207c330cfd74641a228940dea50e36f6673b341ec432f57ec SHA512 (cutadapt-4.6.tar.gz) = b7ab31c6df72d970625edbf3dd0d0970a99c1a044b898449ec059d261db6f64b1b756a8a937217fb3f298cf4cb002c4a8c616402ec7dbc28fc2cc16ea05c2faf Size (cutadapt-4.6.tar.gz) = 250254 bytes @ 1.6 log @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. @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.5 2021/10/26 10:03:43 nia Exp $ d3 3 a5 3 BLAKE2s (cutadapt-3.5.tar.gz) = acfca3b84b2ef7d1cf030b288dd4ea464f8c3243c1566a354f5113a92c2799a1 SHA512 (cutadapt-3.5.tar.gz) = 7ffb2afc1fd57cd30c4c618db0c1c3dde3803bff19709b158537a46c50b4ddc367abf5707e876f139ba5ad1dc18122fa5b69a1db019c03ed7b605cfbb222ef66 Size (cutadapt-3.5.tar.gz) = 303774 bytes @ 1.5 log @biology: Replace RMD160 checksums with BLAKE2s checksums All checksums have been double-checked against existing RMD160 and SHA512 hashes @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.4 2021/10/07 13:19:42 nia Exp $ d3 3 a5 3 BLAKE2s (cutadapt-3.4.tar.gz) = 0013ccc827e0082669442387094d30d78e32d01e3212e2b4d259ec3c006c4f17 SHA512 (cutadapt-3.4.tar.gz) = 8d0556acb2c67146adf68eb208d2ec9701f391e6554d5e1ebaf146a12e3ba02c68b01856c254c94917ba9e919df26ece97a2c41ea386747e1c495eecbf4b2e0c Size (cutadapt-3.4.tar.gz) = 295282 bytes @ 1.4 log @biology: Remove SHA1 hashes for distfiles @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.3 2021/03/31 09:23:56 adam Exp $ d3 1 a3 1 RMD160 (cutadapt-3.4.tar.gz) = 2208111797c90defebb6a220f60b95eb3a7a3efe @ 1.3 log @py-cutadapt: updated to 3.4 v3.4 (2021-03-30) ----------------- * :issue:`481`: An experimental single-file Windows executable of Cutadapt is `available for download on the GitHub "releases" page `_. * :issue:`517`: Report correct sequence in info file if read was reverse complemented * :issue:`517`: Added a column to the info file that shows whether the read was reverse-complemented (if ``--revcomp`` was used) * :issue:`320`: Fix (again) "Too many open files" when demultiplexing @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.2 2021/03/08 07:10:56 adam Exp $ a2 1 SHA1 (cutadapt-3.4.tar.gz) = e3ba4d7c62581cfabf0aa8c966dd1bde055ffdde @ 1.2 log @py-cutadapt: updated to 3.3 v3.3: * :issue:`504`: Fix a crash on Windows. * :issue:`490`: When ``--rename`` is used with ``--revcomp``, disable adding the ``rc`` suffix to reads that were reverse-complemented. * Also, there is now a ``{rc}` template variable for the ``--rename`` option, which is replaced with "rc" if the read was reverse-complemented (and the empty string if not). * :issue:`512`: Fix issue :issue:`128` once more (the “Reads written” figure in the report incorrectly included both trimmed and untrimmed reads if ``--untrimmed-output`` was used). * :issue:`515`: The report is now send to stderr if any output file is written to stdout @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.1 2021/02/08 01:55:23 bacon Exp $ d3 4 a6 4 SHA1 (cutadapt-3.3.tar.gz) = aab2e1ed047c58cbe354b4ac1a4def1c83bf8f8c RMD160 (cutadapt-3.3.tar.gz) = fc7617f33a4d35327af5013b8a7df0df431365a7 SHA512 (cutadapt-3.3.tar.gz) = d8895453455aff31c613a4e031559c08646ce2bf072d85ed7b195e5863700a02a1ed44bfb409b63849aadf1db7cf40dea33d0ead4f056307365dc91aa6c93234 Size (cutadapt-3.3.tar.gz) = 294579 bytes @ 1.1 log @biology/py-cutadapt: import py38-cutadapt-3.2 Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. @ text @d1 1 a1 1 $NetBSD$ d3 4 a6 4 SHA1 (cutadapt-3.2.tar.gz) = 11b2545862c4e9a655a279f951b15558b1617506 RMD160 (cutadapt-3.2.tar.gz) = e04f8be21e118c760dc03d80544c1d4f7135f985 SHA512 (cutadapt-3.2.tar.gz) = 97ab1cadc3bd1585012c0aba916b0031d8b13bff1f1894f4548b6f7bfa20b5f2d598c499664d755a81be57e36fd5c712f36df77cfcd1f2b28a4f27990ee0b56c Size (cutadapt-3.2.tar.gz) = 292702 bytes @