head 1.6; access; symbols pkgsrc-2023Q4:1.5.0.10 pkgsrc-2023Q4-base:1.5 pkgsrc-2023Q3:1.5.0.8 pkgsrc-2023Q3-base:1.5 pkgsrc-2023Q2:1.5.0.6 pkgsrc-2023Q2-base:1.5 pkgsrc-2023Q1:1.5.0.4 pkgsrc-2023Q1-base:1.5 pkgsrc-2022Q4:1.5.0.2 pkgsrc-2022Q4-base:1.5 pkgsrc-2022Q3:1.4.0.8 pkgsrc-2022Q3-base:1.4 pkgsrc-2022Q2:1.4.0.6 pkgsrc-2022Q2-base:1.4 pkgsrc-2022Q1:1.4.0.4 pkgsrc-2022Q1-base:1.4 pkgsrc-2021Q4:1.4.0.2 pkgsrc-2021Q4-base:1.4 pkgsrc-2021Q3:1.2.0.4 pkgsrc-2021Q3-base:1.2 pkgsrc-2021Q2:1.2.0.2 pkgsrc-2021Q2-base:1.2 pkgsrc-2021Q1:1.1.0.2 pkgsrc-2021Q1-base:1.1; locks; strict; comment @# @; 1.6 date 2024.02.10.13.07.54; author bacon; state Exp; branches; next 1.5; commitid 6EUdCCvK4axa6TXE; 1.5 date 2022.11.14.10.39.40; author wiz; state Exp; branches; next 1.4; commitid F5xOmsuMEt9vQE1E; 1.4 date 2021.10.26.10.03.43; author nia; state Exp; branches; next 1.3; commitid R64ULQLy8JYkZieD; 1.3 date 2021.10.07.13.19.42; author nia; state Exp; branches; next 1.2; commitid CQ422EVgQgYxGSbD; 1.2 date 2021.05.21.11.38.13; author adam; state Exp; branches; next 1.1; commitid CQXmIEIRZfDJA0UC; 1.1 date 2021.02.08.01.52.24; author bacon; state Exp; branches; next ; commitid jSrv5kTOa0Y5DQGC; desc @@ 1.6 log @biology/py-dnaio: Update to 1.2.0 Numerous bug fixes and enhancements since 0.9.1 Changes: https://github.com/marcelm/dnaio/tags @ text @$NetBSD$ BLAKE2s (dnaio-1.2.0.tar.gz) = 798b8c22234423de1c9f088cb5bc2b8b6a5fd2999b1021dfa07d1bab2d1fe48e SHA512 (dnaio-1.2.0.tar.gz) = 049d97e73c327b2370fa5500a4fbe3a560eed24d37e1203553a8427dc7c17efc1c6efcbd46e7dd1291fc0ebe2e2d830d6184d3d7bd150c873472505093d3752d Size (dnaio-1.2.0.tar.gz) = 58225 bytes @ 1.5 log @py-dnaio: update to 0.9.1. v0.9.1 (2022-08-01) ------------------- * :pr:`85`: macOS wheels are now also built as part of the release procedure. * :pr:`81`: API documentation improvements and minor code refactors for readability. v0.9.0 (2022-05-17) ------------------- * :pr:`79`: Added a `records_are_mates` function to be used for checking whether three or more records are mates of each other (by checking the ID). * :pr:`74`, :pr:`68`: Made FASTQ parsing faster by implementing the check for ASCII using SSE vector instructions. * :pr:`72`: Added a `tutorial `_. v0.8.0 (2022-03-26) ------------------- * Preliminary documentation is available at . * :pr:`53`: Renamed ``Sequence`` to `SequenceRecord`. The previous name is still available as an alias so that existing code will continue to work. * When reading a FASTQ file, there is now a check that ensures that all characters are ASCII. * Function ``record_names_match`` is deprecated, use `SequenceRecord.is_mate` instead. * Dropped Python 3.6 support as it is end-of-life. v0.7.1 (2022-01-26) ------------------- * :pr:`34`: Fix parsing of FASTA files that just contain a comment and no reads v0.7.0 (2022-01-17) ------------------- * @@rhpvorderman contributed many performance improvements in :pr:`15`, :pr:`17`, :pr:`18`, :pr:`20`, :pr:`21`, :pr:`22`, :pr:`23`. Reading and writing FASTQ files and reading of paired-end FASTQ files was sped up significantly. For example, reading uncompressed FASTQ is 50% faster (!) than before. * :pr:`28`: Windows support added v0.6.0 (2021-09-28) ------------------- * :pr:`12`: Improve FASTQ writing speed twofold (thanks to @@rhpvorderman) v0.5.2 (2021-09-07) ------------------- * :issue:`7`: Ignore a trailing "3" in the read id @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.4 2021/10/26 10:03:43 nia Exp $ d3 3 a5 3 BLAKE2s (dnaio-0.9.1.tar.gz) = 7c5ec560b4efba83d73bbcfdbfcd582b38e118f84e58dcd1701b0e63af314a2b SHA512 (dnaio-0.9.1.tar.gz) = c5975451fd458030a2626e4e85607232c7d169a4b6dabe88830006eea326a810c77955e7d104d30ddd4af5fe552fc10c292ef475a74f84d7e9f03bd9164b1993 Size (dnaio-0.9.1.tar.gz) = 41594 bytes @ 1.4 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 1.3 2021/10/07 13:19:42 nia Exp $ d3 3 a5 3 BLAKE2s (dnaio-0.5.1.tar.gz) = 9eb6348e5dc2dacc625a8d005c929c312bca78ff7ca063573c1c3a55b8f599fc SHA512 (dnaio-0.5.1.tar.gz) = 127e3dcc8291c21e8adce71211692e9c2284d49df336bb923c53fc5fea7dcb9d9b9f047f95642f3300240dac3d43cf6e987b3148b4ffa239d70f3b6c7ef043a5 Size (dnaio-0.5.1.tar.gz) = 126820 bytes @ 1.3 log @biology: Remove SHA1 hashes for distfiles @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.2 2021/05/21 11:38:13 adam Exp $ d3 1 a3 1 RMD160 (dnaio-0.5.1.tar.gz) = fb03fe045f77db1316905e31dc822810f83b1240 @ 1.2 log @py-dnaio: updated to 0.5.1 v0.5.1 Add py.typed and distribute .pyi files @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.1 2021/02/08 01:52:24 bacon Exp $ a2 1 SHA1 (dnaio-0.5.1.tar.gz) = 7c48b05dcfd7d20267f938123b7ce7c37d59eee8 @ 1.1 log @biology/py-dnaio: import py38-dnaio-0.5.0 dnaio is a Python 3 library for fast input and output of FASTQ and FASTA files. It supports paired-end data in separate files, interleaved paired-end in a single file and compression using gzip, bzip, and xz. @ text @d1 1 a1 1 $NetBSD$ d3 4 a6 4 SHA1 (dnaio-0.5.0.tar.gz) = 466b533b83ef34baab0492199264a6d88d34be57 RMD160 (dnaio-0.5.0.tar.gz) = 731c217d956cf03088851579bd364d510b8222ec SHA512 (dnaio-0.5.0.tar.gz) = 2e6a0dd04558b70ee08a81fd1d118525734df52701735cc27bab4c423c2030ec2fb6e83ddf02c491e1eb250c471d230b8fa72993c3a20ae844716c9542059c67 Size (dnaio-0.5.0.tar.gz) = 126321 bytes @