head 1.15; access; symbols pkgsrc-2023Q4:1.15.0.18 pkgsrc-2023Q4-base:1.15 pkgsrc-2023Q3:1.15.0.16 pkgsrc-2023Q3-base:1.15 pkgsrc-2023Q2:1.15.0.14 pkgsrc-2023Q2-base:1.15 pkgsrc-2023Q1:1.15.0.12 pkgsrc-2023Q1-base:1.15 pkgsrc-2022Q4:1.15.0.10 pkgsrc-2022Q4-base:1.15 pkgsrc-2022Q3:1.15.0.8 pkgsrc-2022Q3-base:1.15 pkgsrc-2022Q2:1.15.0.6 pkgsrc-2022Q2-base:1.15 pkgsrc-2022Q1:1.15.0.4 pkgsrc-2022Q1-base:1.15 pkgsrc-2021Q4:1.15.0.2 pkgsrc-2021Q4-base:1.15 pkgsrc-2021Q3:1.13.0.48 pkgsrc-2021Q3-base:1.13 pkgsrc-2021Q2:1.13.0.46 pkgsrc-2021Q2-base:1.13 pkgsrc-2021Q1:1.13.0.44 pkgsrc-2021Q1-base:1.13 pkgsrc-2020Q4:1.13.0.42 pkgsrc-2020Q4-base:1.13 pkgsrc-2020Q3:1.13.0.40 pkgsrc-2020Q3-base:1.13 pkgsrc-2020Q2:1.13.0.36 pkgsrc-2020Q2-base:1.13 pkgsrc-2020Q1:1.13.0.16 pkgsrc-2020Q1-base:1.13 pkgsrc-2019Q4:1.13.0.38 pkgsrc-2019Q4-base:1.13 pkgsrc-2019Q3:1.13.0.34 pkgsrc-2019Q3-base:1.13 pkgsrc-2019Q2:1.13.0.32 pkgsrc-2019Q2-base:1.13 pkgsrc-2019Q1:1.13.0.30 pkgsrc-2019Q1-base:1.13 pkgsrc-2018Q4:1.13.0.28 pkgsrc-2018Q4-base:1.13 pkgsrc-2018Q3:1.13.0.26 pkgsrc-2018Q3-base:1.13 pkgsrc-2018Q2:1.13.0.24 pkgsrc-2018Q2-base:1.13 pkgsrc-2018Q1:1.13.0.22 pkgsrc-2018Q1-base:1.13 pkgsrc-2017Q4:1.13.0.20 pkgsrc-2017Q4-base:1.13 pkgsrc-2017Q3:1.13.0.18 pkgsrc-2017Q3-base:1.13 pkgsrc-2017Q2:1.13.0.14 pkgsrc-2017Q2-base:1.13 pkgsrc-2017Q1:1.13.0.12 pkgsrc-2017Q1-base:1.13 pkgsrc-2016Q4:1.13.0.10 pkgsrc-2016Q4-base:1.13 pkgsrc-2016Q3:1.13.0.8 pkgsrc-2016Q3-base:1.13 pkgsrc-2016Q2:1.13.0.6 pkgsrc-2016Q2-base:1.13 pkgsrc-2016Q1:1.13.0.4 pkgsrc-2016Q1-base:1.13 pkgsrc-2015Q4:1.13.0.2 pkgsrc-2015Q4-base:1.13 pkgsrc-2015Q3:1.12.0.32 pkgsrc-2015Q3-base:1.12 pkgsrc-2015Q2:1.12.0.30 pkgsrc-2015Q2-base:1.12 pkgsrc-2015Q1:1.12.0.28 pkgsrc-2015Q1-base:1.12 pkgsrc-2014Q4:1.12.0.26 pkgsrc-2014Q4-base:1.12 pkgsrc-2014Q3:1.12.0.24 pkgsrc-2014Q3-base:1.12 pkgsrc-2014Q2:1.12.0.22 pkgsrc-2014Q2-base:1.12 pkgsrc-2014Q1:1.12.0.20 pkgsrc-2014Q1-base:1.12 pkgsrc-2013Q4:1.12.0.18 pkgsrc-2013Q4-base:1.12 pkgsrc-2013Q3:1.12.0.16 pkgsrc-2013Q3-base:1.12 pkgsrc-2013Q2:1.12.0.14 pkgsrc-2013Q2-base:1.12 pkgsrc-2013Q1:1.12.0.12 pkgsrc-2013Q1-base:1.12 pkgsrc-2012Q4:1.12.0.10 pkgsrc-2012Q4-base:1.12 pkgsrc-2012Q3:1.12.0.8 pkgsrc-2012Q3-base:1.12 pkgsrc-2012Q2:1.12.0.6 pkgsrc-2012Q2-base:1.12 pkgsrc-2012Q1:1.12.0.4 pkgsrc-2012Q1-base:1.12 pkgsrc-2011Q4:1.12.0.2 pkgsrc-2011Q4-base:1.12 pkgsrc-2011Q3:1.9.0.24 pkgsrc-2011Q3-base:1.9 pkgsrc-2011Q2:1.9.0.22 pkgsrc-2011Q2-base:1.9 pkgsrc-2011Q1:1.9.0.20 pkgsrc-2011Q1-base:1.9 pkgsrc-2010Q4:1.9.0.18 pkgsrc-2010Q4-base:1.9 pkgsrc-2010Q3:1.9.0.16 pkgsrc-2010Q3-base:1.9 pkgsrc-2010Q2:1.9.0.14 pkgsrc-2010Q2-base:1.9 pkgsrc-2010Q1:1.9.0.12 pkgsrc-2010Q1-base:1.9 pkgsrc-2009Q4:1.9.0.10 pkgsrc-2009Q4-base:1.9 pkgsrc-2009Q3:1.9.0.8 pkgsrc-2009Q3-base:1.9 pkgsrc-2009Q2:1.9.0.6 pkgsrc-2009Q2-base:1.9 pkgsrc-2009Q1:1.9.0.4 pkgsrc-2009Q1-base:1.9 pkgsrc-2008Q4:1.9.0.2 pkgsrc-2008Q4-base:1.9 pkgsrc-2008Q3:1.8.0.18 pkgsrc-2008Q3-base:1.8 cube-native-xorg:1.8.0.16 cube-native-xorg-base:1.8 pkgsrc-2008Q2:1.8.0.14 pkgsrc-2008Q2-base:1.8 cwrapper:1.8.0.12 pkgsrc-2008Q1:1.8.0.10 pkgsrc-2008Q1-base:1.8 pkgsrc-2007Q4:1.8.0.8 pkgsrc-2007Q4-base:1.8 pkgsrc-2007Q3:1.8.0.6 pkgsrc-2007Q3-base:1.8 pkgsrc-2007Q2:1.8.0.4 pkgsrc-2007Q2-base:1.8 pkgsrc-2007Q1:1.8.0.2 pkgsrc-2007Q1-base:1.8 pkgsrc-2006Q4:1.7.0.2 pkgsrc-2006Q4-base:1.7 pkgsrc-2006Q3:1.6.0.4 pkgsrc-2006Q3-base:1.6 pkgsrc-2006Q2:1.6.0.2 pkgsrc-2006Q2-base:1.6 pkgsrc-2006Q1:1.5.0.2 pkgsrc-2006Q1-base:1.5 pkgsrc-2005Q4:1.4.0.6 pkgsrc-2005Q4-base:1.4 pkgsrc-2005Q3:1.4.0.4 pkgsrc-2005Q3-base:1.4 pkgsrc-2005Q2:1.4.0.2 pkgsrc-2005Q2-base:1.4 pkgsrc-2005Q1:1.3.0.2 pkgsrc-2005Q1-base:1.3 pkgsrc-2004Q4:1.2.0.2 pkgsrc-2004Q4-base:1.2 pkgsrc-2004Q3:1.1.1.1.0.8 pkgsrc-2004Q3-base:1.1.1.1 pkgsrc-2004Q2:1.1.1.1.0.6 pkgsrc-2004Q2-base:1.1.1.1 pkgsrc-2004Q1:1.1.1.1.0.4 pkgsrc-2004Q1-base:1.1.1.1 pkgsrc-2003Q4:1.1.1.1.0.2 pkgsrc-2003Q4-base:1.1.1.1 pkgsrc-base:1.1.1.1 TNF:1.1.1; locks; strict; comment @# @; 1.15 date 2021.10.26.10.03.41; author nia; state Exp; branches; next 1.14; commitid R64ULQLy8JYkZieD; 1.14 date 2021.10.07.13.19.40; author nia; state Exp; branches; next 1.13; commitid CQ422EVgQgYxGSbD; 1.13 date 2015.11.02.18.42.22; author agc; state Exp; branches; next 1.12; commitid QWWynLrDLYuI4yHy; 1.12 date 2011.11.25.20.09.01; author joerg; state Exp; branches; next 1.11; 1.11 date 2011.11.24.14.24.34; author joerg; state Exp; branches; next 1.10; 1.10 date 2011.11.23.22.37.44; author marino; state Exp; branches; next 1.9; 1.9 date 2008.10.11.22.01.13; author schwarz; state Exp; branches; next 1.8; 1.8 date 2007.01.18.19.13.10; author rillig; state Exp; branches; next 1.7; 1.7 date 2006.12.06.16.52.20; author joerg; state Exp; branches; next 1.6; 1.6 date 2006.04.19.16.50.36; author joerg; state Exp; branches; next 1.5; 1.5 date 2006.01.29.19.31.43; author schwarz; state Exp; branches; next 1.4; 1.4 date 2005.06.19.01.13.23; author kristerw; state Exp; branches; next 1.3; 1.3 date 2005.02.22.21.28.55; author agc; state Exp; branches; next 1.2; 1.2 date 2004.12.05.15.24.54; author cube; state Exp; branches; next 1.1; 1.1 date 2003.09.27.22.24.57; author jschauma; state Exp; branches 1.1.1.1; next ; 1.1.1.1 date 2003.09.27.22.24.57; author jschauma; state Exp; branches; next ; desc @@ 1.15 log @biology: Replace RMD160 checksums with BLAKE2s checksums All checksums have been double-checked against existing RMD160 and SHA512 hashes @ text @$NetBSD: distinfo,v 1.14 2021/10/07 13:19:40 nia Exp $ BLAKE2s (MUMmer3.20.tar.gz) = 76714f0e739d1953cab3f01a70f22fe029ec65b4af367135e7d5c720a7014a5c SHA512 (MUMmer3.20.tar.gz) = 7c80bb605d57739809eb1b1cf8a579d72048e510362237d9ba64e21be18cc663769cda5dabc287832e59fb62804df34bc8336c2b42474466e7ee1e126848aecd Size (MUMmer3.20.tar.gz) = 3155446 bytes SHA1 (patch-aa) = 0f719a55e3c4f2994060f2b3f3ab4eb83519376f SHA1 (patch-ab) = af42da79fd287786cb83efa9c9b4fc8025abd728 SHA1 (patch-ac) = 7f0f16bdd83bc80833f1ffdcfe1bad7c2ee76eec SHA1 (patch-ad) = 7c86aeabb92fbe0879b096da00d987d3b5693f9c @ 1.14 log @biology: Remove SHA1 hashes for distfiles @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.13 2015/11/02 18:42:22 agc Exp $ d3 1 a3 1 RMD160 (MUMmer3.20.tar.gz) = 7e5fefef359c6a6ee49f2ebf14dc18caa19f48fb @ 1.13 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 1.12 2011/11/25 20:09:01 joerg Exp $ a2 1 SHA1 (MUMmer3.20.tar.gz) = 68d6742de93d8524236ccf538f32ba8bb4edf7cc @ 1.12 log @Remove concurrently created patch. @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.11 2011/11/24 14:24:34 joerg Exp $ d5 1 @ 1.11 log @Fix build with GCC 4.5 @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.10 2011/11/23 22:37:44 marino Exp $ a9 1 SHA1 (patch-src_tigr_show-diff.cc) = af646127f9baf48fb1316fcaa7f29139d1aa6a9f @ 1.10 log @biology/mummer: Put sort function in scope Add header for sort, DragonFly's compiler needs it. No PKGREVISION bump required. @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.9 2008/10/11 22:01:13 schwarz Exp $ d10 1 @ 1.9 log @updated to MUMmer3.20 @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.8 2007/01/18 19:13:10 rillig Exp $ d9 1 @ 1.8 log @Updated mummer to 3.19. Changes since 3.18: - More documentation. @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.7 2006/12/06 16:52:20 joerg Exp $ d3 4 a6 4 SHA1 (MUMmer3.19.tar.gz) = 8906bab6bd43b307461de8b5f44122a115799533 RMD160 (MUMmer3.19.tar.gz) = 54f3c692efb8bde7762c48186919754f2a8c178c Size (MUMmer3.19.tar.gz) = 3141991 bytes SHA1 (patch-aa) = e40b6538b259475def39cd8008af37d0a08e1555 a8 1 SHA1 (patch-ad) = 0804b2c966d7035c23444c4f72e1d93e45805bcf @ 1.7 log @Fix path to csh in scripts. Bump revision. @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.6 2006/04/19 16:50:36 joerg Exp $ d3 4 a6 4 SHA1 (MUMmer3.18.tar.gz) = 484846f7ff68e19bc0e0deca92254fd423947a9f RMD160 (MUMmer3.18.tar.gz) = 7361a90d28e2432a9163e0745ab854dfd31cf306 Size (MUMmer3.18.tar.gz) = 3069437 bytes SHA1 (patch-aa) = 707f0466ac20b58feb22a5fd525f5f8d9df31dac @ 1.6 log @Fix build with newer versions of GNU make. @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.5 2006/01/29 19:31:43 schwarz Exp $ d6 2 a7 2 SHA1 (patch-aa) = 369c4646b01acb4607aae933b70a08448331c3e6 SHA1 (patch-ab) = 8548bc11a6d43b489ea9af5dbca584ce0d2750c9 @ 1.5 log @ Updated biology/mummer to release 3.18. Changes include: - MUMmer now resides at Sourceforge - new tools such as delta-filter - more extensive html documentation and examples - bug fixes @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.4 2005/06/19 01:13:23 kristerw Exp $ d9 1 @ 1.4 log @Prevent paths to the build directories from being included in the package. Bump PKGREVISION. @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.3 2005/02/22 21:28:55 agc Exp $ d3 4 a6 4 SHA1 (MUMmer3.15.tar.gz) = c8907b0b2010e3a8d07fff0dde570c12d9cf8dea RMD160 (MUMmer3.15.tar.gz) = 223135f09c8795f7fab5219f07c7047f114056df Size (MUMmer3.15.tar.gz) = 660102 bytes SHA1 (patch-aa) = bf64019cbbfa53c1883641b28186146cd7c0a946 d8 1 @ 1.3 log @Add RMD160 digests in addition to the SHA1 ones. @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.2 2004/12/05 15:24:54 cube Exp $ d7 1 @ 1.2 log @Update to version 3.15. From David Price in PR#28305. 3.05 - Added -k option to show-coords to only display the best frame for overlapping PROmer alignments. Added --[no]optimize option to nucmer and promer to allow alignment score optimization to be turned off, i.e allow alignments to extend to the ends of sequences rather than backtracking to optimize the alignment score. Updated docs. 3.06 - Added -F and -h option to mummer. Changed -mumcand option to -mumreference, but left deprecated -mumcand option available. Added -maxmatch option to mummer, and changed default behavior of all applicable programs to -mumreference (nucmer, promer and mummer). Added -w (screen width) option to show-aligns. Updated documentation with all of these changes. 3.07 - Added the 'mapview' plotting utility and appropriate documentation. Fixed origin wrap shadowing bug in show-tiling when using the -c option. NUCmer and PROmer now convert to absolute paths to avoid ambiguity. 3.08 - Added MUMmer examples web docs which gives brief walkthroughs 3.10 - Now Mac OSX compatible. Added -R option to show-tiling. 3.11 - Fixed bug show-tiling -R option. Added some mapview changes. Fixed the issue with mummerplot being to faint. 3.12 - Added the --nosimplify option to nucmer for repeat searching. Fixed a bug in nucmer and promer. Fixed rounding issue in show-coords. Updated citations. 3.13 - Added -d, -g, -G and -o options to show-coords and updated documentation. Fixed bug in show-tiling -R 3.14 - Fixed gcc3 compilation bug 3.15 - Fixed --nooptimize in nuc/promer. @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.1.1.1 2003/09/27 22:24:57 jschauma Exp $ d4 1 @ 1.1 log @Initial revision @ text @d1 1 a1 1 $NetBSD$ d3 3 a5 3 SHA1 (MUMmer3.04.tar.gz) = e0f17d535a857bd9b3059d5d0a951621f89041b2 Size (MUMmer3.04.tar.gz) = 835629 bytes SHA1 (patch-aa) = 39253c79e7239365dfdcee46c410f234a23c6df0 @ 1.1.1.1 log @Initial import of mummer, one of the many packages provided by brook at biology dot nmsu dot edu and his team at NMSU. Mummer is a system for aligning whole genome sequences. Using an efficient data structure called a suffix tree, the system is able rapidly to align sequences containing millions of nucleotides whether in complete or draft form. MUMmer can also align incomplete genomes; it handles the 100s or 1000s of contigs from a shotgun sequencing project with ease, and will align them to another set of contigs or a genome using the NUCmer program included with the system. @ text @@