[med-svn] [Git][med-team/libbioparser-dev][master] 13 commits: Reset to unreleased to run routine-update
Andreas Tille
gitlab at salsa.debian.org
Sun May 3 15:39:11 BST 2020
Andreas Tille pushed to branch master at Debian Med / libbioparser-dev
Commits:
3c4509d5 by Andreas Tille at 2020-05-03T16:16:33+02:00
Reset to unreleased to run routine-update
- - - - -
5b48657e by Andreas Tille at 2020-05-03T16:17:01+02:00
New upstream version 2.1.2
- - - - -
16bf6921 by Andreas Tille at 2020-05-03T16:17:01+02:00
routine-update: New upstream version
- - - - -
20ceebb9 by Andreas Tille at 2020-05-03T16:17:04+02:00
Update upstream source from tag 'upstream/2.1.2'
Update to upstream version '2.1.2'
with Debian dir b906d1eae7c47b4ade439074c076eb9f9f0bb502
- - - - -
ec45e02a by Andreas Tille at 2020-05-03T16:17:04+02:00
routine-update: Standards-Version: 4.5.0
- - - - -
ab9e171b by Andreas Tille at 2020-05-03T16:17:09+02:00
routine-update: Add salsa-ci file
- - - - -
20829d59 by Andreas Tille at 2020-05-03T16:17:09+02:00
routine-update: Rules-Requires-Root: no
- - - - -
e325e5ea by Andreas Tille at 2020-05-03T16:17:10+02:00
Remove unnecessary Team Upload line in changelog.
Fixes: lintian: unnecessary-team-upload
See-also: https://lintian.debian.org/tags/unnecessary-team-upload.html
- - - - -
25adf00b by Andreas Tille at 2020-05-03T16:17:13+02:00
Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse.
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
Fixes: lintian: upstream-metadata-missing-repository
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html
- - - - -
917171a6 by Andreas Tille at 2020-05-03T16:17:13+02:00
Remove obsolete field Name from debian/upstream/metadata (already present in machine-readable debian/copyright).
- - - - -
243b9b01 by Andreas Tille at 2020-05-03T16:20:20+02:00
Upload to unstable
- - - - -
b32f6c89 by Andreas Tille at 2020-05-03T16:34:31+02:00
DEP3
- - - - -
2b9ffb18 by Andreas Tille at 2020-05-03T16:34:40+02:00
Team upload
- - - - -
6 changed files:
- debian/changelog
- debian/control
- debian/patches/gcc10.patch
- + debian/salsa-ci.yml
- debian/upstream/metadata
- include/bioparser/bioparser.hpp
Changes:
=====================================
debian/changelog
=====================================
@@ -1,9 +1,20 @@
-libbioparser-dev (2.1.1-2) unstable; urgency=medium
+libbioparser-dev (2.1.2-1) unstable; urgency=medium
- * Team upload.
+ [ Etienne Mollier ]
+ * Team upload
* Add fix for ftbfs with gcc-10 (Closes: #959465)
- -- Etienne Mollier <etienne.mollier at mailoo.org>
+ [ Andreas Tille ]
+ * New upstream version
+ * Standards-Version: 4.5.0 (routine-update)
+ * Add salsa-ci file (routine-update)
+ * Rules-Requires-Root: no (routine-update)
+ * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
+ Repository-Browse.
+ * Remove obsolete field Name from debian/upstream/metadata (already
+ present in machine-readable debian/copyright).
+
+ -- Étienne Mollier <etienne.mollier at mailoo.org> Sun, 03 May 2020 16:17:01 +0200
libbioparser-dev (2.1.1-1) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -7,10 +7,11 @@ Build-Depends: debhelper-compat (= 12),
cmake,
zlib1g-dev,
libgtest-dev (>> 1.8.0-10~)
-Standards-Version: 4.4.0
+Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/libibioparser-dev
Vcs-Git: https://salsa.debian.org/med-team/libbioparser-dev.git
Homepage: https://github.com/rvaser/bioparser/
+Rules-Requires-Root: no
Package: libbioparser-dev
Architecture: all
=====================================
debian/patches/gcc10.patch
=====================================
@@ -1,3 +1,8 @@
+From: Étienne Mollier <etienne.mollier at mailoo.org>
+Date: Sun, 3 May 2020 10:30:58 +0200
+Bug-Debian: https://bugs.debian.org/959465
+Description: Fix gcc-10 build error
+
--- libbioparser-dev.orig/include/bioparser/bioparser.hpp
+++ libbioparser-dev/include/bioparser/bioparser.hpp
@@ -10,6 +10,7 @@
=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
=====================================
debian/upstream/metadata
=====================================
@@ -1 +1,4 @@
-Name: bioparser
+Bug-Database: https://github.com/rvaser/bioparser/issues
+Bug-Submit: https://github.com/rvaser/bioparser/issues/new
+Repository: https://github.com/rvaser/bioparser.git
+Repository-Browse: https://github.com/rvaser/bioparser
=====================================
include/bioparser/bioparser.hpp
=====================================
@@ -17,7 +17,7 @@
namespace bioparser {
-static const std::string version = "v2.1.1";
+static const std::string version = "v2.1.2";
/*!
* @brief Parser absctract class
@@ -727,6 +727,11 @@ inline bool SamParser<T>::parse(std::vector<std::unique_ptr<T>>& dst,
quality_length = 0;
auto create_T = [&] () -> void {
+ if (this->storage_[0] == '@') { // header
+ storage_ptr = 0;
+ return;
+ }
+
this->storage_[storage_ptr] = 0;
rightStrip(&(this->storage_[0]), storage_ptr);
@@ -828,11 +833,6 @@ inline bool SamParser<T>::parse(std::vector<std::unique_ptr<T>>& dst,
for (; this->buffer_ptr_ < this->buffer_bytes_; ++this->buffer_ptr_) {
auto c = this->buffer_[this->buffer_ptr_];
if (c == '\n') {
- if (this->buffer_[begin_ptr] == '@') {
- begin_ptr = this->buffer_ptr_ + 1;
- storage_ptr = 0;
- continue;
- }
std::memcpy(&this->storage_[storage_ptr],
&this->buffer_[begin_ptr],
this->buffer_ptr_ - begin_ptr);
View it on GitLab: https://salsa.debian.org/med-team/libbioparser-dev/-/compare/ab7634a04f237875db8ae20c9a70ee59992fa9b6...2b9ffb18d42172cee06dc2af64b2de6b6c9bf642
--
View it on GitLab: https://salsa.debian.org/med-team/libbioparser-dev/-/compare/ab7634a04f237875db8ae20c9a70ee59992fa9b6...2b9ffb18d42172cee06dc2af64b2de6b6c9bf642
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