Andreas Tille pushed to branch master at Debian Med / plink2
Commits: 0d168792 by Andreas Tille at 2022-12-12T09:23:45+01:00 See https://lists.debian.org/debian-med/2022/08/msg00025.html - - - - - 02d8b737 by Andreas Tille at 2022-12-12T09:32:31+01:00 Fix watch file - - - - - 358a17ba by Andreas Tille at 2022-12-12T09:33:29+01:00 New upstream version 2.00~a3.5-220809+dfsg - - - - - 851217d2 by Andreas Tille at 2022-12-12T09:33:32+01:00 Update upstream source from tag 'upstream/2.00_a3.5-220809+dfsg' Update to upstream version '2.00~a3.5-220809+dfsg' with Debian dir 4a1a2ec178da65c6d8e00399937d3dcc8743cdfb - - - - - e1479acc by Andreas Tille at 2022-12-12T09:47:47+01:00 routine-update: Ready to upload to unstable - - - - - 6 changed files: - debian/changelog - debian/patches/baseline - debian/watch - include/plink2_base.h - plink2.cc - plink2_merge.cc Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,10 @@ +plink2 (2.00~a3.5-220809+dfsg-1) unstable; urgency=medium + + * Team upload. + * Fix watch file (seems we are at ~a3.5 released at 220809) + + -- Andreas Tille <[email protected]> Mon, 12 Dec 2022 09:35:02 +0100 + plink2 (2.00~a3.3-220801+dfsg-1) unstable; urgency=medium * Team upload. ===================================== debian/patches/baseline ===================================== @@ -8,7 +8,7 @@ Forwarded: not-needed # BASEFLAGS=-g -DZSTD_MULTITHREAD -DSTATIC_ZSTD -BASEFLAGS=-g -mavx2 -mbmi -mbmi2 -mfma -mlzcnt -DZSTD_MULTITHREAD -+BASEFLAGS=-g -DZSTD_MULTITHREAD ++BASEFLAGS=-g -mfma -DZSTD_MULTITHREAD # BASEFLAGS=-g -msse4.2 -DZSTD_MULTITHREAD include Makefile.src ===================================== debian/watch ===================================== @@ -1,3 +1,10 @@ version=4 -opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,uversionmangle=s/(\d\S+)/2.00~a3.3-$1/,repack,compression=xz" \ - https://www.cog-genomics.org/plink/2.0/ /static/bin/plink2_src_(\d\S+)\.zip + +opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,uversionmangle=s/(\d\S+)/2.00~a3.5-$1/" \ + https://www.cog-genomics.org/plink/2.0/dev /static/bin/plink2_src_(\d\S+)\.zip + +# There are newer tags on github than on cog-genomics.org but this is a mixed tarball of version 1.9 and 2.0 +# The "version" ~a3.5 above was guessed from the github tags at the date encoded in the zip file name +#opts="repacksuffix=+dfsg,dversionmangle=auto,uversionmangle=s/a/~a/,filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE@-$1.tar.gz%" \ +# https://github.com/chrchang/plink-ng/tags (?:.*?/)?v?@ANY_VERSION@@ARCHIVE_EXT@ + ===================================== include/plink2_base.h ===================================== @@ -713,7 +713,7 @@ CONSTI32(kBytesPerVec, 32); // However, processor power management, numeric libraries, and my AVX2 code // should improve over time. There will probably come a time where switching // to 32-byte fp is worthwhile. -#define FVEC_32 +// #define FVEC_32 // bleah, have to define these here, vector_size doesn't see enum values typedef uintptr_t VecW __attribute__ ((vector_size (32))); ===================================== plink2.cc ===================================== @@ -44,7 +44,7 @@ namespace plink2 { #endif -static const char ver_str[] = "PLINK v2.00a3.4" +static const char ver_str[] = "PLINK v2.00a3.5" #ifdef NOLAPACK "NL" #endif @@ -72,7 +72,7 @@ static const char ver_str[] = "PLINK v2.00a3.4" #ifdef USE_MKL " Intel" #endif - " (1 Aug 2022)"; + " (9 Aug 2022)"; static const char ver_str2[] = // include leading space if day < 10, so character length stays the same " " ===================================== plink2_merge.cc ===================================== @@ -5539,6 +5539,8 @@ PglErr MergePgenVariantNoTmpLocked(SamePosPvarRecord** same_id_records, const Al } else { reterr = PgrGetMDp(sample_include, cur_mrp->pssi, read_sample_ct, read_variant_uidx, pgrp, pgvp); } + // bugfix (9 Aug 2022) + ZeroTrailingNyps(read_sample_ct, pgvp->genovec); if (unlikely(reterr)) { PgenErrPrintNV(reterr, read_variant_uidx); goto MergePgenVariantNoTmpLocked_ret_1; View it on GitLab: https://salsa.debian.org/med-team/plink2/-/compare/3966fd8542ef1088dd35eed6bac3fac3943fb94c...e1479accf4cf0cd6cd67879e7d8b743b957cbe02 -- View it on GitLab: https://salsa.debian.org/med-team/plink2/-/compare/3966fd8542ef1088dd35eed6bac3fac3943fb94c...e1479accf4cf0cd6cd67879e7d8b743b957cbe02 You're receiving this email because of your account on salsa.debian.org.
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