Andreas Tille pushed to branch master at Debian Med / sambamba
Commits: dfa0243a by Andreas Tille at 2018-08-30T05:51:04Z Fix normalize(weight) - - - - - 9b509f8f by Andreas Tille at 2018-08-30T05:54:25Z Should close #907489 but it does not work - wait for new upstream release - - - - - 3 changed files: - debian/changelog - + debian/patches/03_fix_normalize.patch - debian/patches/series Changes: ===================================== debian/changelog ===================================== @@ -2,6 +2,8 @@ sambamba (0.6.7-3) UNRELEASED; urgency=medium * Point Vcs fields to salsa.debian.org * Standards-Version: 4.2.1 + * Fix normalize(weight) (applied patch from upstream) + Should close #907489 but it does not work - wait for new upstream release -- Andreas Tille <[email protected]> Tue, 28 Aug 2018 20:07:55 +0200 ===================================== debian/patches/03_fix_normalize.patch ===================================== @@ -0,0 +1,47 @@ +From: Pjotr Prins <[email protected]> +Origin: https://github.com/biod/sambamba/commit/cb170d641c21f5aabeb04cedab3ced5b7262d007 +Date: Fri, 27 Jul 2018 23:28:29 +0000 +Bug-Debian: https://bugs.debian.org/907489 +Subject: [PATCH] Fixes normalize(weight) + +/gnu/store/4snsi4vg06bdfi6qhdjfbhss16kvzxj7-ldc-1.10.0/include/d/std/numeric.d(1845): +Error: read-modify-write operations are not allowed for shared variables. Use core.atomic.atomicOp!"+="(s, e) instead. +--- + Makefile | 2 +- + Makefile.guix | 6 +++--- + sambamba/merge.d | 8 ++++++-- + 3 files changed, 10 insertions(+), 6 deletions(-) + +--- a/Makefile ++++ b/Makefile +@@ -1,5 +1,5 @@ + D_COMPILER=dmd +-D_FLAGS=--compiler=dmd -IBioD -IundeaD/src -g -d#-O -release -inline # -version=serial ++D_FLAGS=--compiler=dmd -I../BioD -IBioD -IundeaD/src -g -d#-O -release -inline # -version=serial + LDMD=ldmd2 + + STATIC_LIB_PATH=-Lhtslib -Llz4/lib +--- a/sambamba/merge.d ++++ b/sambamba/merge.d +@@ -1,6 +1,7 @@ + /* + This file is part of Sambamba. + Copyright (C) 2012-2016 Artem Tarasov <[email protected]> ++ Copyright (C) 2012-2017 Pjotr Prins <[email protected]> + + Sambamba is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by +@@ -403,8 +404,11 @@ int merge_main(string[] args) { + alias ReturnType!(BamReader.readsWithProgress!withoutOffsets) AlignmentRangePB; + auto alignmentranges_with_file_ids = new Tuple!(AlignmentRangePB, size_t)[files.length]; + +- auto weights = cast(shared)array(map!(pipe!(getSize, to!float))(filenames)); +- normalize(cast()weights); ++ // auto weights = cast(shared)array(map!(pipe!(getSize, to!float))(filenames)); ++ auto weights1 = array(map!(pipe!(getSize, to!float))(filenames)); ++ normalize(weights1); ++ // auto weights = cast(shared)weights1; ++ immutable weights = cast(immutable)weights1; + + foreach (i; 0 .. files.length) { + alignmentranges_with_file_ids[i] = tuple( ===================================== debian/patches/series ===================================== @@ -1,2 +1,3 @@ 01_add_meson.patch disable-assert.patch +03_fix_normalize.patch View it on GitLab: https://salsa.debian.org/med-team/sambamba/compare/0dbfbf9eb8785bd300dcc61023be3782108d1eb7...9b509f8f4924cfa9dc65dc9c4b2367e22f2a1129 -- View it on GitLab: https://salsa.debian.org/med-team/sambamba/compare/0dbfbf9eb8785bd300dcc61023be3782108d1eb7...9b509f8f4924cfa9dc65dc9c4b2367e22f2a1129 You're receiving this email because of your account on salsa.debian.org.
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