first commit

bamviewer.cpp

@@ -0,0 +1,48 @@
+#include "bamviewer.h"
+
+BamViewer::BamViewer(QObject *parent)
+{
+
+
+
+}
+
+void BamViewer::setFilename(const QString &filename)
+{
+    QFileInfo info(filename);
+    mFilename = info.absoluteFilePath();
+
+    QString s = "/home/sacha/exemple.sam";
+    qDebug()<<QFile::exists(s);
+
+    BamFileIn file(s.toStdString().c_str());
+
+
+    BamHeader header;
+    readHeader(header,file);
+
+   while (!atEnd(file))
+   {
+       BamAlignmentRecord record;
+
+       readRecord(record, file);
+
+       qDebug()<<record.beginPos;
+
+
+   }
+
+
+
+
+
+}
+
+void BamViewer::paintEvent(QPaintEvent *event)
+{
+    Q_UNUSED(event)
+    QPainter painter(viewport());
+
+
+
+}

bamviewer.h

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+#ifndef BAMVIEWER_H
+#define BAMVIEWER_H
+#include <QAbstractScrollArea>
+#include <QPainter>
+#include <QtCore>
+#include <zlib.h>
+
+#include "seqan/bam_io.h"
+#include <iostream>
+
+#define SEQAN_HAS_ZLIB 1
+
+using namespace seqan;
+
+class BamViewer : public QAbstractScrollArea
+{
+public:
+    BamViewer(QObject * parent = nullptr);
+
+    void setFilename(const QString& filename);
+
+protected:
+
+    void paintEvent(QPaintEvent * event)  override;
+
+private:
+    QString mFilename;
+
+};
+
+#endif // BAMVIEWER_H

bamviewer.pro

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+#-------------------------------------------------
+#
+# Project created by QtCreator 2018-01-21T16:57:25
+#
+#-------------------------------------------------
+
+QT       += core gui
+
+greaterThan(QT_MAJOR_VERSION, 4): QT += widgets
+
+TARGET = bamviewer
+TEMPLATE = app
+
+# The following define makes your compiler emit warnings if you use
+# any feature of Qt which has been marked as deprecated (the exact warnings
+# depend on your compiler). Please consult the documentation of the
+# deprecated API in order to know how to port your code away from it.
+DEFINES += QT_DEPRECATED_WARNINGS
+
+# You can also make your code fail to compile if you use deprecated APIs.
+# In order to do so, uncomment the following line.
+# You can also select to disable deprecated APIs only up to a certain version of Qt.
+#DEFINES += QT_DISABLE_DEPRECATED_BEFORE=0x060000    # disables all the APIs deprecated before Qt 6.0.0
+
+CONFIG+= c++14
+
+SOURCES += \
+        main.cpp \
+        mainwindow.cpp \
+    bamviewer.cpp
+
+HEADERS += \
+        mainwindow.h \
+    bamviewer.h
+
+FORMS += \
+        mainwindow.ui
+
+LIBS+= -lz

main.cpp

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+#include "mainwindow.h"
+#include <QApplication>
+
+int main(int argc, char *argv[])
+{
+    QApplication a(argc, argv);
+    MainWindow w;
+    w.show();
+
+    return a.exec();
+}

mainwindow.cpp

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+#include "mainwindow.h"
+#include "ui_mainwindow.h"
+
+MainWindow::MainWindow(QWidget *parent) :
+    QMainWindow(parent)
+{
+
+    mViewer = new BamViewer;
+
+    mViewer->setFilename("/home/sacha/exemple.bam");
+
+
+    setCentralWidget(mViewer);
+}
+
+MainWindow::~MainWindow()
+{
+}

mainwindow.h

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+#ifndef MAINWINDOW_H
+#define MAINWINDOW_H
+
+#include <QMainWindow>
+#include "bamviewer.h"
+
+
+class MainWindow : public QMainWindow
+{
+    Q_OBJECT
+
+public:
+    explicit MainWindow(QWidget *parent = 0);
+    ~MainWindow();
+
+private:
+    BamViewer * mViewer;
+};
+
+#endif // MAINWINDOW_H

mainwindow.ui

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+<ui version="4.0">
+ <class>MainWindow</class>
+ <widget class="QMainWindow" name="MainWindow" >
+  <property name="geometry" >
+   <rect>
+    <x>0</x>
+    <y>0</y>
+    <width>400</width>
+    <height>300</height>
+   </rect>
+  </property>
+  <property name="windowTitle" >
+   <string>MainWindow</string>
+  </property>
+  <widget class="QMenuBar" name="menuBar" />
+  <widget class="QToolBar" name="mainToolBar" />
+  <widget class="QWidget" name="centralWidget" />
+  <widget class="QStatusBar" name="statusBar" />
+ </widget>
+ <layoutDefault spacing="6" margin="11" />
+ <pixmapfunction></pixmapfunction>
+ <resources/>
+ <connections/>
+</ui>

seqan/LICENSE

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+Copyright (c) 2006-2016, Knut Reinert, FU Berlin
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+    * Redistributions of source code must retain the above copyright
+      notice, this list of conditions and the following disclaimer.
+    * Redistributions in binary form must reproduce the above copyright
+      notice, this list of conditions and the following disclaimer in the
+      documentation and/or other materials provided with the distribution.
+    * Neither the name of Knut Reinert or the FU Berlin nor the names of
+      its contributors may be used to endorse or promote products derived
+      from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+DAMAGE.
+