[med-svn] [Git][med-team/libbioparser-dev][master] 6 commits: Fix watchfile to detect new versions on github
Andreas Tille (@tille)
gitlab at salsa.debian.org
Fri Oct 15 07:44:32 BST 2021
Andreas Tille pushed to branch master at Debian Med / libbioparser-dev
Commits:
714586ed by Andreas Tille at 2021-10-15T08:08:48+02:00
Fix watchfile to detect new versions on github
- - - - -
58dccf73 by Andreas Tille at 2021-10-15T08:08:53+02:00
New upstream version 3.0.15
- - - - -
50e06d56 by Andreas Tille at 2021-10-15T08:08:53+02:00
routine-update: New upstream version
- - - - -
75737d51 by Andreas Tille at 2021-10-15T08:08:56+02:00
Update upstream source from tag 'upstream/3.0.15'
Update to upstream version '3.0.15'
with Debian dir ecc2aac829a17e0d9cece45a869c50b9e91242e4
- - - - -
4c26c6a2 by Andreas Tille at 2021-10-15T08:08:56+02:00
routine-update: Standards-Version: 4.6.0
- - - - -
1b77cbd3 by Andreas Tille at 2021-10-15T08:44:15+02:00
Build-Depends: libbiosoup-dev
- - - - -
9 changed files:
- + .github/workflows/bioparser.yml
- − .travis.yml
- CMakeLists.txt
- README.md
- debian/changelog
- debian/control
- debian/watch
- include/bioparser/fastq_parser.hpp
- include/bioparser/parser.hpp
Changes:
=====================================
.github/workflows/bioparser.yml
=====================================
@@ -0,0 +1,51 @@
+name: bioparser CI
+
+on:
+ push:
+ pull_request:
+ branches:
+ - master
+
+env:
+ BUILD_TYPE: Release
+
+jobs:
+ test:
+ strategy:
+ matrix:
+ compiler:
+ - g++
+ - g++-4.8
+ - clang++
+ - clang++-4.0
+
+ runs-on: ubuntu-18.04
+
+ steps:
+ - uses: actions/checkout at v2
+
+ - if: ${{ matrix.compiler == 'g++-4.8' }}
+ name: Setup GCC
+ uses: egor-tensin/setup-gcc at v1
+ with:
+ version: "4.8"
+ platform: x64
+
+ - if: ${{ matrix.compiler == 'clang++-4.0' }}
+ name: Setup Clang
+ uses: egor-tensin/setup-clang at v1
+ with:
+ version: "4.0"
+ platform: x64
+
+ - name: Configure CMake
+ run: cmake -B ${{ github.workspace }}/build -DCMAKE_BUILD_TYPE=${{ env.BUILD_TYPE }}
+ env:
+ CXX: ${{ matrix.compiler }}
+
+ - name: Build
+ run: cmake --build ${{ github.workspace }}/build --config ${{ env.BUILD_TYPE }}
+
+ - name: Test
+ working-directory: ${{ github.workspace }}/build
+ run: bin/bioparser_test
=====================================
.travis.yml deleted
=====================================
@@ -1,43 +0,0 @@
-language: cpp
-
-matrix:
- include:
- - name: "GCC 4.8 (Linux)" # GCC 4.8.5 & CMake 3.12.4
- os: linux
- dist: xenial
- addons:
- apt:
- sources:
- - ubuntu-toolchain-r-test
- packages:
- - g++-4.8
- env:
- - SET_COMPILER="export CC=gcc-4.8 && export CXX=g++-4.8"
-
- - name: "Clang 3.5 (Linux)" # Clang 3.5.2 & CMake 3.12.4
- os: linux
- dist: xenial
- addons:
- apt:
- packages:
- - clang-3.5
- env:
- - SET_COMPILER="export CC=clang-3.5 && export CXX=clang++-3.5"
-
- - name: "Clang Xcode 9.4 (OSX)" # Clang 9.4.1 & CMake 3.15.5
- os: osx
- osx_image: xcode9.4
-
-before_install:
- - eval "${SET_COMPILER}"
-
-install:
- - mkdir build && cd build
- - cmake -DCMAKE_BUILD_TYPE=Release .. && make
-
-script:
- - ./bin/bioparser_test
-
-notifications:
- email:
- on_failure: always
=====================================
CMakeLists.txt
=====================================
@@ -1,6 +1,6 @@
cmake_minimum_required(VERSION 3.11)
-project(bioparser VERSION 3.0.13
+project(bioparser VERSION 3.0.15
LANGUAGES CXX
DESCRIPTION "Bioparser is a c++ header only parsing library for several formats in bioinformatics (FASTA/Q, MHAP/PAF/SAM), with support for zlib compressed files.")
=====================================
README.md
=====================================
@@ -1,7 +1,7 @@
# Bioparser
[](https://github.com/rvaser/bioparser/releases/latest)
-[](https://travis-ci.com/rvaser/bioparser)
+
Bioparser is a c++ header only parsing library for several bioinformatics formats (FASTA/Q, MHAP/PAF/SAM), with support for zlib compressed files..
@@ -38,8 +38,8 @@ If you are not using CMake, include the appropriate header file directly to your
- (optional) cmake 3.11+
###### Hidden
-- (bioparser_test) biosoup 0.10.0
-- (bioparser_test) googletest 1.10.0
+- (bioparser_test) rvaser/biosoup 0.10.0
+- (bioparser_test) google/googletest 1.10.0
## Examples
=====================================
debian/changelog
=====================================
@@ -1,10 +1,17 @@
-libbioparser-dev (3.0.13-1) UNRELEASED; urgency=medium
+libbioparser-dev (3.0.15-1) unstable; urgency=medium
+ [ Michael R. Crusoe ]
* Team upload.
* New upstream version
- TODO: wait for libbiosoup-dev to enter the archive
- -- Michael R. Crusoe <crusoe at debian.org> Mon, 08 Mar 2021 17:10:31 +0100
+ [ Andreas Tille ]
+ * Fix watchfile to detect new versions on github
+ * Standards-Version: 4.6.0 (routine-update)
+ * Build-Depends: libbiosoup-dev
+
+ TODO: wait for libbiosoup-dev to enter the archive
+
+ -- Andreas Tille <tille at debian.org> Fri, 15 Oct 2021 08:08:59 +0200
libbioparser-dev (3.0.12-1) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -6,8 +6,9 @@ Priority: optional
Build-Depends: debhelper-compat (= 13),
cmake,
zlib1g-dev,
- libgtest-dev (>> 1.8.0-10~)
-Standards-Version: 4.5.1
+ libgtest-dev,
+ libbiosoup-dev
+Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/libbioparser-dev
Vcs-Git: https://salsa.debian.org/med-team/libbioparser-dev.git
Homepage: https://github.com/rvaser/bioparser/
=====================================
debian/watch
=====================================
@@ -1,3 +1,3 @@
version=4
-https://github.com/rvaser/bioparser/releases .*/archive/@ANY_VERSION@@ARCHIVE_EXT@
+https://github.com/rvaser/bioparser/releases .*/@ANY_VERSION@@ARCHIVE_EXT@
=====================================
include/bioparser/fastq_parser.hpp
=====================================
@@ -85,7 +85,7 @@ class FastqParser: public Parser<T> {
is_quality = true;
quality_ptr = this->storage_ptr();
} else if (is_quality &&
- this->storage_ptr() - quality_ptr == comment_ptr - data_ptr) {
+ this->storage_ptr() - quality_ptr >= comment_ptr - data_ptr) {
is_quality = false;
is_name = true;
create_T();
=====================================
include/bioparser/parser.hpp
=====================================
@@ -7,6 +7,7 @@
#include <cctype>
#include <cstdint>
#include <cstring>
+#include <limits>
#include <memory>
#include <stdexcept>
#include <string>
@@ -82,11 +83,15 @@ class Parser { // Parser factory
return buffer_bytes_ < buffer_.size();
}
- void Store(std::uint32_t count, bool strip = false) {
+ void Store(std::size_t count, bool strip = false) {
if (buffer_ptr_ + count > buffer_.size()) {
throw std::invalid_argument(
"[bioparser::Parser::Store] error: buffer overflow");
}
+ if (storage_ptr_ + count > std::numeric_limits<std::uint32_t>::max()) {
+ throw std::invalid_argument(
+ "[bioparser::Parser::Store] error: storage overflow");
+ }
if (storage_ptr_ + count > storage_.size()) {
storage_.resize(2 * storage_.size());
}
View it on GitLab: https://salsa.debian.org/med-team/libbioparser-dev/-/compare/0f8747db179d1b7abcbce1957928320c52182ef7...1b77cbd3bcbe424c592d0765e7b9cdc64c0876f7
--
View it on GitLab: https://salsa.debian.org/med-team/libbioparser-dev/-/compare/0f8747db179d1b7abcbce1957928320c52182ef7...1b77cbd3bcbe424c592d0765e7b9cdc64c0876f7
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