[med-svn] [Git][med-team/libbioparser-dev][upstream] New upstream version 3.0.15

[Andreas Tille (@tille)]

Andreas Tille pushed to branch upstream at Debian Med / libbioparser-dev


Commits:
58dccf73 by Andreas Tille at 2021-10-15T08:08:53+02:00
New upstream version 3.0.15
- - - - -


6 changed files:

- + .github/workflows/bioparser.yml
- − .travis.yml
- CMakeLists.txt
- README.md
- 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
 
 [![Latest GitHub release](https://img.shields.io/github/release/rvaser/bioparser.svg)](https://github.com/rvaser/bioparser/releases/latest)
-[![Build status for gcc/clang](https://travis-ci.com/rvaser/bioparser.svg?branch=master)](https://travis-ci.com/rvaser/bioparser)
+![Build status for gcc/clang](https://github.com/rvaser/bioparser/actions/workflows/bioparser.yml/badge.svg)
 
 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
 


=====================================
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/-/commit/58dccf73ed064f18637c24f264f98e0ab900a468

-- 
View it on GitLab: https://salsa.debian.org/med-team/libbioparser-dev/-/commit/58dccf73ed064f18637c24f264f98e0ab900a468
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