Examples & Code Snippets

Sections in alphabetical order.

Bioinformatics

Filter .bam files for a specific chromosome and start positions of reads: script which converts a .bam into a .sam file, filters the reads based on chromosome and read start position, converts back into a sorted .bam and creates the .bai index.

Linux

Git Undo Reset Hard: Recover Staged Files Which Got Deleted By Git Reset –Hard (Linux): how to recover staged but uncommitted files which got accidentally deleted by git reset --hard

Check SSH-KEY Fingerprint: how to check ssh-key fingerprints and why it matters

How To Write Desktop Files (Linux): how to write desktop files for yourself or other users to provide more convenient access to applications

Recover file extensions for multiple files (Linux): add file extensions to files based on mime-types

Misc

My First Post

Multimedia

VLC: Play folder and sub-folders in random order using repeat-all: small code-snippet showing how to use VLC commandline for playing the music of a folder and its subfolders in random order using repeat all.

Ubuntu 14.04 install Cmus and Lyvi: how to install the commandline music player Cmus and the lyric fetcher Lyvi in Ubuntu 14.04

Delete metadata of images before uploading or sharing: why and how to delete metadata on images before sharing

to_gif: A Bash Script for Easy JPG to GIF Conversion: how to easily create an aligned gif from images

Programming

Auto-Scroll-Down in Swing GUI Progress-/Status-Window: explanation and example implementation of a logging/status window which scrolls down automatically when reaching the bottom of the window using a Java-Swing GUI

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