[med-svn] [Git][med-team/sambamba][master] 2 commits: Fix normalize(weight)

[Andreas Tille]

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 <tille at debian.org>  Tue, 28 Aug 2018 20:07:55 +0200
 


=====================================
debian/patches/03_fix_normalize.patch
=====================================
@@ -0,0 +1,47 @@
+From: Pjotr Prins <pjotr.public01 at thebird.nl>
+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 <lomereiter at gmail.com>
++    Copyright (C) 2012-2017    Pjotr Prins <pjotr.prins at thebird.nl>
+ 
+     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
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