head 1.7; access; symbols pkgsrc-2023Q4:1.7.0.18 pkgsrc-2023Q4-base:1.7 pkgsrc-2023Q3:1.7.0.16 pkgsrc-2023Q3-base:1.7 pkgsrc-2023Q2:1.7.0.14 pkgsrc-2023Q2-base:1.7 pkgsrc-2023Q1:1.7.0.12 pkgsrc-2023Q1-base:1.7 pkgsrc-2022Q4:1.7.0.10 pkgsrc-2022Q4-base:1.7 pkgsrc-2022Q3:1.7.0.8 pkgsrc-2022Q3-base:1.7 pkgsrc-2022Q2:1.7.0.6 pkgsrc-2022Q2-base:1.7 pkgsrc-2022Q1:1.7.0.4 pkgsrc-2022Q1-base:1.7 pkgsrc-2021Q4:1.7.0.2 pkgsrc-2021Q4-base:1.7 pkgsrc-2021Q3:1.5.0.48 pkgsrc-2021Q3-base:1.5 pkgsrc-2021Q2:1.5.0.46 pkgsrc-2021Q2-base:1.5 pkgsrc-2021Q1:1.5.0.44 pkgsrc-2021Q1-base:1.5 pkgsrc-2020Q4:1.5.0.42 pkgsrc-2020Q4-base:1.5 pkgsrc-2020Q3:1.5.0.40 pkgsrc-2020Q3-base:1.5 pkgsrc-2020Q2:1.5.0.36 pkgsrc-2020Q2-base:1.5 pkgsrc-2020Q1:1.5.0.16 pkgsrc-2020Q1-base:1.5 pkgsrc-2019Q4:1.5.0.38 pkgsrc-2019Q4-base:1.5 pkgsrc-2019Q3:1.5.0.34 pkgsrc-2019Q3-base:1.5 pkgsrc-2019Q2:1.5.0.32 pkgsrc-2019Q2-base:1.5 pkgsrc-2019Q1:1.5.0.30 pkgsrc-2019Q1-base:1.5 pkgsrc-2018Q4:1.5.0.28 pkgsrc-2018Q4-base:1.5 pkgsrc-2018Q3:1.5.0.26 pkgsrc-2018Q3-base:1.5 pkgsrc-2018Q2:1.5.0.24 pkgsrc-2018Q2-base:1.5 pkgsrc-2018Q1:1.5.0.22 pkgsrc-2018Q1-base:1.5 pkgsrc-2017Q4:1.5.0.20 pkgsrc-2017Q4-base:1.5 pkgsrc-2017Q3:1.5.0.18 pkgsrc-2017Q3-base:1.5 pkgsrc-2017Q2:1.5.0.14 pkgsrc-2017Q2-base:1.5 pkgsrc-2017Q1:1.5.0.12 pkgsrc-2017Q1-base:1.5 pkgsrc-2016Q4:1.5.0.10 pkgsrc-2016Q4-base:1.5 pkgsrc-2016Q3:1.5.0.8 pkgsrc-2016Q3-base:1.5 pkgsrc-2016Q2:1.5.0.6 pkgsrc-2016Q2-base:1.5 pkgsrc-2016Q1:1.5.0.4 pkgsrc-2016Q1-base:1.5 pkgsrc-2015Q4:1.5.0.2 pkgsrc-2015Q4-base:1.5 pkgsrc-2015Q3:1.4.0.42 pkgsrc-2015Q3-base:1.4 pkgsrc-2015Q2:1.4.0.40 pkgsrc-2015Q2-base:1.4 pkgsrc-2015Q1:1.4.0.38 pkgsrc-2015Q1-base:1.4 pkgsrc-2014Q4:1.4.0.36 pkgsrc-2014Q4-base:1.4 pkgsrc-2014Q3:1.4.0.34 pkgsrc-2014Q3-base:1.4 pkgsrc-2014Q2:1.4.0.32 pkgsrc-2014Q2-base:1.4 pkgsrc-2014Q1:1.4.0.30 pkgsrc-2014Q1-base:1.4 pkgsrc-2013Q4:1.4.0.28 pkgsrc-2013Q4-base:1.4 pkgsrc-2013Q3:1.4.0.26 pkgsrc-2013Q3-base:1.4 pkgsrc-2013Q2:1.4.0.24 pkgsrc-2013Q2-base:1.4 pkgsrc-2013Q1:1.4.0.22 pkgsrc-2013Q1-base:1.4 pkgsrc-2012Q4:1.4.0.20 pkgsrc-2012Q4-base:1.4 pkgsrc-2012Q3:1.4.0.18 pkgsrc-2012Q3-base:1.4 pkgsrc-2012Q2:1.4.0.16 pkgsrc-2012Q2-base:1.4 pkgsrc-2012Q1:1.4.0.14 pkgsrc-2012Q1-base:1.4 pkgsrc-2011Q4:1.4.0.12 pkgsrc-2011Q4-base:1.4 pkgsrc-2011Q3:1.4.0.10 pkgsrc-2011Q3-base:1.4 pkgsrc-2011Q2:1.4.0.8 pkgsrc-2011Q2-base:1.4 pkgsrc-2011Q1:1.4.0.6 pkgsrc-2011Q1-base:1.4 pkgsrc-2010Q4:1.4.0.4 pkgsrc-2010Q4-base:1.4 pkgsrc-2010Q3:1.4.0.2 pkgsrc-2010Q3-base:1.4 pkgsrc-2010Q2:1.3.0.42 pkgsrc-2010Q2-base:1.3 pkgsrc-2010Q1:1.3.0.40 pkgsrc-2010Q1-base:1.3 pkgsrc-2009Q4:1.3.0.38 pkgsrc-2009Q4-base:1.3 pkgsrc-2009Q3:1.3.0.36 pkgsrc-2009Q3-base:1.3 pkgsrc-2009Q2:1.3.0.34 pkgsrc-2009Q2-base:1.3 pkgsrc-2009Q1:1.3.0.32 pkgsrc-2009Q1-base:1.3 pkgsrc-2008Q4:1.3.0.30 pkgsrc-2008Q4-base:1.3 pkgsrc-2008Q3:1.3.0.28 pkgsrc-2008Q3-base:1.3 cube-native-xorg:1.3.0.26 cube-native-xorg-base:1.3 pkgsrc-2008Q2:1.3.0.24 pkgsrc-2008Q2-base:1.3 cwrapper:1.3.0.22 pkgsrc-2008Q1:1.3.0.20 pkgsrc-2008Q1-base:1.3 pkgsrc-2007Q4:1.3.0.18 pkgsrc-2007Q4-base:1.3 pkgsrc-2007Q3:1.3.0.16 pkgsrc-2007Q3-base:1.3 pkgsrc-2007Q2:1.3.0.14 pkgsrc-2007Q2-base:1.3 pkgsrc-2007Q1:1.3.0.12 pkgsrc-2007Q1-base:1.3 pkgsrc-2006Q4:1.3.0.10 pkgsrc-2006Q4-base:1.3 pkgsrc-2006Q3:1.3.0.8 pkgsrc-2006Q3-base:1.3 pkgsrc-2006Q2:1.3.0.6 pkgsrc-2006Q2-base:1.3 pkgsrc-2006Q1:1.3.0.4 pkgsrc-2006Q1-base:1.3 pkgsrc-2005Q4:1.3.0.2 pkgsrc-2005Q4-base:1.3 pkgsrc-2005Q3:1.2.0.4 pkgsrc-2005Q3-base:1.2 pkgsrc-2005Q2:1.2.0.2 pkgsrc-2005Q2-base:1.2 pkgsrc-base:1.1.1.1 TNF:1.1.1; locks; strict; comment @# @; 1.7 date 2021.10.26.10.03.40; author nia; state Exp; branches; next 1.6; commitid R64ULQLy8JYkZieD; 1.6 date 2021.10.07.13.19.40; author nia; state Exp; branches; next 1.5; commitid CQ422EVgQgYxGSbD; 1.5 date 2015.11.02.18.42.21; author agc; state Exp; branches; next 1.4; commitid QWWynLrDLYuI4yHy; 1.4 date 2010.09.19.07.13.37; author obache; state Exp; branches; next 1.3; 1.3 date 2005.12.13.15.24.09; author joerg; state Exp; branches; next 1.2; 1.2 date 2005.05.25.11.31.56; author wiz; state Exp; branches; next 1.1; 1.1 date 2005.03.26.17.05.03; author minskim; state Exp; branches 1.1.1.1; next ; 1.1.1.1 date 2005.03.26.17.05.03; author minskim; state Exp; branches; next ; desc @@ 1.7 log @biology: Replace RMD160 checksums with BLAKE2s checksums All checksums have been double-checked against existing RMD160 and SHA512 hashes @ text @$NetBSD: distinfo,v 1.6 2021/10/07 13:19:40 nia Exp $ BLAKE2s (lucy1.20.tar.gz) = 808f1116d0ef7515fea97c88a26eeab0a1b6c7c4118af9b982b8a4ff4636678f SHA512 (lucy1.20.tar.gz) = 8e182f8ecb84f374a2f40e39645dde724520c87b78bc9cfd4975ea32ad69fceccc65a899010401692f96f297e07b5f89061ab9ad8975fafd3e99c57e7ae579e2 Size (lucy1.20.tar.gz) = 1457619 bytes SHA1 (patch-aa) = 2e37aaf7cad62d0183f8555b4f2bd8824b10468b SHA1 (patch-ab) = 638e512be7fc526cbd37950f9156ccab46b9f228 @ 1.6 log @biology: Remove SHA1 hashes for distfiles @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.5 2015/11/02 18:42:21 agc Exp $ d3 1 a3 1 RMD160 (lucy1.20.tar.gz) = de6f9a787f9bd63b8d297beb2ecdc9793e3c183d @ 1.5 log @Add SHA512 digests for distfiles for biology category. Existing SHA1 digests verified, all found to be the same on the machine holding the existing distfiles (morden). Existing SHA1 digests retained for now as an audit trail. @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.4 2010/09/19 07:13:37 obache Exp $ a2 1 SHA1 (lucy1.20.tar.gz) = 890006f550efd06745e7156359ee8b519d3b5f62 @ 1.4 log @Update lucy to 1.20. Based on PR#43777 by Kamel Derouiche, with some clean up by me. Version 1.20, 9/3/2008. This version fixes a bug that caused lucy to fail when there was too much information on the FASTA header lines in the input files. Lucy had a 256 character buffer for reading lines from the input files. If any FASTA header lines were longer than 256 characters, the remaining characters would get read as part of the FASTA sequence. The solution implemented in this version is simply to increase the buffer size to 4096 characters. While that still leaves the potential for the same error to occur with extremely long header lines, the limitation that this entails seems reasonable, and this should fix the problem for all pratical purposes. --------------------------------------------------------------------- Version 1.19, 12/30/2003. This version fixes a bug that could cause sequences to be rejected incorrectly in the vector detection step (phase 6). Because of the way that lucy compares "tags" in the target sequence with "tags" in the vector sequence, some bases in the target sequence could get counted more than once in the tally of bases that match the vector sequence. In rare instances, this could cause the sequence to exceed the minimum threshold for rejection, as a result of random sequence similarity. The reporting of the CLB range in the -debug output file has also been changed. If the CLB range begins with the first base of the sequence, then the left coordinate of the CLB range will be reported as 1 (instead of 0). The range "CLB 0 0" still indicates an empty CLB range. @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.3 2005/12/13 15:24:09 joerg Exp $ d5 1 @ 1.3 log @Don't hard-wire -lpthread, use PTHREAD_*. @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.2 2005/05/25 11:31:56 wiz Exp $ d3 3 a5 3 SHA1 (lucy-1.18p.tar.gz) = 93ff9002f7eb69815497633007952ede9ca63e66 RMD160 (lucy-1.18p.tar.gz) = db6f8dd8d3fdab81bfcc7f1a4f558fd908c6d309 Size (lucy-1.18p.tar.gz) = 1456857 bytes @ 1.2 log @Add RMD160 checksum. @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.1.1.1 2005/03/26 17:05:03 minskim Exp $ d6 1 a6 1 SHA1 (patch-aa) = 89acea1ef9398cb8fefed57e4d28a925644fb9f9 @ 1.1 log @Initial revision @ text @d1 1 a1 1 $NetBSD$ d4 1 @ 1.1.1.1 log @Import lucy from pkgsrc-wip. Packaged by David Price and modified by me. A Sequence Cleanup Program. Lucy is a utility that prepares raw DNA sequence fragments for sequence assembly,possibly using the TIGR Assembler. The cleanup process includes quality assessment, confidence reassurance, vector trimming and vector removal. The primary advantage of Lucy over other similar utilities is that it is a fully integrated, stand alone program. @ text @@