Merge branch 'devel' into htslib

- AbstractSequenceReader have now a virtual constructor
- ui accept *.bam and *.ubam file

Author: natir

.coveralls.yml

@@ -0,0 +1 @@
+repo_token: Dj6d3Ke8T5Ikm96bvMvronbJV1AI1Cu9I

.travis.yml

@@ -37,7 +37,7 @@ script:
   - cp ./usr/share/icons/hicolor/48x48/apps/fastqt.png .
   - cp ./usr/share/applications/fastqt.desktop .
   - cd .. 
-  - wget -c "https://github.com/probonopd/linuxdeployqt/releases/download/3/linuxdeployqt-3-x86_64.AppImage" 
+  - wget -c "https://github.com/probonopd/linuxdeployqt/releases/download/continuous/linuxdeployqt-continuous-x86_64.AppImage" 
   - chmod a+x linuxdeployqt*.AppImage
   - unset QTDIR; unset QT_PLUGIN_PATH ; unset LD_LIBRARY_PATH
   - ./linuxdeployqt*.AppImage ./appdir/usr/bin/* -bundle-non-qt-libs

AUTHORS

@@ -1,11 +1,23 @@
 FastQt is a free software created by labsquare team. Labsquare is a community of developers which aims to develop bioinformatics user interface for clinical usage.
 Here is the list of authors and contributor of FastQt.
 
-Sacha Schutz <sacha@labsquare.org>
-Pierre Marijon <pierre@marijon.fr>
-Jérémie Roquet <jroquet@arkanosis.net>
+## Developers
+@dridk Sacha Schutz <sacha@labsquare.org>
+@natir Pierre Marijon<pierre@marijon.fr>
+@arkanosis Jérémie Roquet<jroquet@arkanosis.net>
 
-FastQt is a clone of FastQC. I would like to mention and thanks the author of FastQC Pierre Lindenbaum for his outstanding work. 
+## Packagers
+@StuntsPT Francisco Pina-Martins
+@probonopd
+
+## Translators
+@JuneBS June Sallou
+
+## Designers
+@beardedpayton Payton Burdette
+
+
+FastQt is a clone of FastQC. I would like to mention and thanks authors of FastQC for their outstanding work.
 
 I also thanks the genetics laboratory at Brest hospital for giving me time to develop bioinformatics tools. 
 https://www.chu-brest.fr/fr/notre-offre-soins/nos-specialites/biologie/genetique-moleculaire-histocompatibilite

CHANGELOG

@@ -3,7 +3,21 @@ All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](http://keepachangelog.com/) 
 and this project adheres to [Semantic Versioning](http://semver.org/)
-.
+
+<<<<<<< HEAD
+## [0.2.3] - 2017-14-03
+### Changed
+- Fix delay time before running. Now analysis doesn't wait to run
+- Remove debugging message
+- Fix bug when exporting PNG data.
+=======
+## [0.2.3] - 2017-29-03
+### Changed
+- Exporting file displays a progress dialog
+- Add recent menu
+
+>>>>>>> devel
+
 ## [0.2.2] - 2017-03-03
 ### Changed
 - Fix Crash when reading .xz file 
@@ -15,7 +29,6 @@ and this project adheres to [Semantic Versioning](http://semver.org/)
 ### Changed
 - Remove filter of file by extension
 
-
 ## [0.2] - 2017-02-10
 ### Changed 
 - Main UI is now a list of analysis 

FastQt.pro

@@ -5,8 +5,9 @@
 #-------------------------------------------------
 QT       += core gui concurrent charts svg
 #QMAKE_CXXFLAGS  += -Ofast
-QMAKE_CXXFLAGS += -std=c++11
-#CONFIG(release, debug|release):DEFINES += QT_NO_DEBUG_OUTPUT
+CONFIG   += c++11
+
+CONFIG(release, debug|release):DEFINES += QT_NO_DEBUG_OUTPUT
 
 
 # METHOD 1 : If KArchive is not installed as a Qt Module then copy to your Qt installation :

QFontIcon/qfonticon.cpp

@@ -25,7 +25,7 @@ SOFTWARE.
 #include "qfonticon.h"
 #include <QDebug>
 #include <QFontDatabase>
-QFontIcon * QFontIcon::mInstance = Q_NULLPTR;
+QFontIcon * QFontIcon::mInstance = nullptr;
 
 bool QFontIcon::addFont(const QString &filename)
 {

QFontIcon/qfonticon.h

@@ -64,7 +64,7 @@ class QFontIcon : public QObject
     static bool addFont(const QString& filename);
     static QFontIcon * instance();
     // main methods. Return icons from code
-    static QIcon icon(const QChar& code, const QColor& baseColor = QColor(),const QString& family = QString());
+    static QIcon icon(const QChar& code, const QColor& baseColor = QColor(),const QString& family = QStringLiteral());
     // return added fonts
     const QStringList& families() const;
 

README.md

@@ -1,31 +1,36 @@
-#FastQt ![travis](https://api.travis-ci.org/labsquare/fastQt.svg?branch=master) ![Qt](https://img.shields.io/badge/Qt-qmake-green.svg) [![Gitter](https://badges.gitter.im/labsquare/fastQt.svg)](https://gitter.im/labsquare/fastQt?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge)
+# FastQt 
+
+![travis](https://api.travis-ci.org/labsquare/fastQt.svg?branch=master) [![Gitter](https://badges.gitter.im/labsquare/fastQt.svg)](https://gitter.im/labsquare/fastQt?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge) [![Build status](https://ci.appveyor.com/api/projects/status/skmgugijflggfq4x?svg=true)](https://ci.appveyor.com/project/dridk/fastqt) [![Coverage Status](https://coveralls.io/repos/github/labsquare/fastQt/badge.svg?branch=master)](https://coveralls.io/github/labsquare/fastQt?branch=master)   
+
 FastQt is the clone of [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) application ported 
 from Java to [C++/Qt5](https://www.qt.io/) 
 
+
 ![Preview](https://raw.githubusercontent.com/labsquare/fastQt/master/screenshot.gif)
 
-##Installation 
-### Ubuntu
-deb package has not yet ready. But An [AppImage](http://appimage.org/) has been made for Linux x86_64 and has been tested on ubuntu 16.04.  
-You can download it from [here](https://github.com/labsquare/fastQt/releases/download/0.1/fastqt-0.1-linux-x86_64.AppImage) and run it as follow : 
+## Installation 
 
-    chmod +x fastqt-0.1-linux-x86_64.AppImage
-    ./fastqt-0.1-linux-x86_64.AppImage
+### Linux 
+An [AppImage](http://appimage.org/) has been created and should work on recent Linux distribution.     
+Download the last release from [here](https://github.com/labsquare/fastQt/releases/) and run it as follow : 
+
+    chmod +x fastqt-0.2.3-linux-x86_64.AppImage
+    ./fastqt-0.2.3-linux-x86_64.AppImage
 
 ### Archlinux
 There is an AUR package for Archlinux. [Just get it from the AUR](https://aur.archlinux.org/packages/fastqt/).
-    
-    
-Other package will come soon for Windows and MacOS. You can try to compile it anyway.
-    
+ 
+### Windows 
+Windows installer and portable version are avaible [here]( https://github.com/labsquare/fastQt/releases/)
+        
 ## Compilation 
 ### Prerequisites - Install KArchive
-You need to install karchive before compiling FastQt.    
+On Linux, you need to install karchive before compiling FastQt.    
 **From ubuntu** >xenial you can install it from repositories : 
 
      sudo apt install libkf5archive-dev
 
-**From fedoar** >= 24 you can install it from repositories :
+**From fedora** >= 24 you can install it from repositories :
 
     sudo dnf install kf5-karchive-devel
 
@@ -43,14 +48,17 @@ You need to install karchive before compiling FastQt.
     cmake .. -DCMAKE_INSTALL_PREFIX=/usr/
     make 
     sudo make install
+    
+** From Windows **    
+Nothing to do. Compiled library are avaible in win32 directory.  
 
 ### Install Qt >5.7
 
 **From website** : Download Qt > 5.7 from https://www.qt.io/.   
 Don't forget to check QtChart module during installation. 
 
 **From ubuntu** : Qt 5.7 is not yet avaible with ubuntu. But you can add PPA to your software system. 
-For exemple for xenial 
+For exemple from xenial 
 
     sudo add-apt-repository ppa:beineri/opt-qt57-xenial
     sudo apt-get install qt57base qt57charts-no-lgpl
@@ -61,7 +69,7 @@ For exemple for xenial
     sudo dnf install qt5-qtbase-devel qt5-qtcharts-devel 
 
 ### Compile FastQt 
-Be sure you have the correct version of Qt (>5.7) by using qmake. You will find qmake in bin folder where you installed Qt. For exemple, if you installed Qt from ppa:beineri, you will find it under /opt/qt57/bin/qmake. Then launch the compilation from FastQC folder as follow.
+Be sure you have the correct version of Qt (>5.7) by using qmake --version. For exemple, if you have installed Qt from ppa:beineri, you will find it under /opt/qt57/bin/qmake. Then launch the compilation from FastQC folder as follow.
 
      /opt/qt57/bin/qmake --version
      /opt/qt57/bin/qmake 
@@ -70,7 +78,14 @@ Be sure you have the correct version of Qt (>5.7) by using qmake. You will find
 
 ## Usage
 
-You can use FastQt as GUI application or in Command Line Interface.
+FastQt can analyse uncompress and compress fastq files. The following extensions are supported :
+
+- *.fastq
+- *.fastq.gz
+- *.fastq.xz
+- *.fastq.bz2
+
+You can use FastQt as GUI application or as a Command Line Interface.
 
 Some usage example :
 
@@ -80,3 +95,6 @@ fastqt file1.fastq file2.fastq.gz file3.fastq.bzip # File save in file1 file 2 f
 fastqt file1.fastq -o specific_path # Create specific directory for each file in specific_path
 fastqt file1.fastq -t 2 # Fastqt run maximal two process this option is valid for GUI too
 ```
+
+## How to cite FastQt 
+Labsquare Team, et al (2017). FastQt: a quality control tool for high throughput sequence data. Available online at: https://github.com/labsquare/fastQt

analysis/analysis.cpp

@@ -24,7 +24,7 @@ Copyright Copyright 2016-17 Sacha Schutz
 Analysis::Analysis(QObject * parent)
     :QObject(parent)
 {
-    mParentRunner = Q_NULLPTR;
+    mParentRunner = nullptr;
 }
 
 Analysis::~Analysis()
@@ -36,8 +36,8 @@ void Analysis::save(const QString &path)
 {
     QString name = metaObject()->className();
     QDir dir(path);
-    QString svgPath = dir.filePath(QString("%1.svg").arg(name));
-    QString pngPath = dir.filePath(QString("%1.png").arg(name));
+    QString svgPath = dir.filePath(QStringLiteral("%1.svg").arg(name));
+    QString pngPath = dir.filePath(QStringLiteral("%1.png").arg(name));
 
     capture(svgPath);
     capture(pngPath, ImageFormat::PngFormat);

analysis/analysis.h

@@ -48,7 +48,7 @@ class Analysis : public QObject
         Success , Warning, Error, Unknown
     };
 
-    Analysis(QObject * parent = Q_NULLPTR);
+    Analysis(QObject * parent = nullptr);
 
     virtual ~Analysis();
     /*!