Introducing AlnMassage Each good scientific experiment should start with an hypothesis. This is true also for sequencing in the age of NGS. However, often enough the data doesn’t fit the expectations. In this case
Pitiful Bioinformatics strlen(genome): The Pitiful State of Software Engineering in Bioinformatics Genomes are very long strings. This comes to no surprise to anybody, except maybe a few C programmers. The following bug appears only in C programs or bad C++ programs due to the
Pitiful Bioinformatics FASTA: The Pitiful State of Software Engineering in Bioinformatics “A QA Engineer walks into a bar. Orders a beer. Orders 0 beers. Orders 999999999 beers. Orders a lizard. Orders -1 beers. Orders a sfdeljknesv.” FASTA is the simplest file format ever invented
Pitiful Bioinformatics RSPR: The Pitiful State of Software Engineering in Bioinformatics RSPR is a tool to compute a topological distance between two phylogenies. It is an alternative to the Robinson-Foulds distance. The canonical implementation rspr has supports many different algorithms and options. Unfortunately, the
Pitiful Bioinformatics INDELible: The Pitiful State of Software Engineering in Bioinformatics INDELible is one of the most sophisticated simulators for sequence evolution. It supports plenty of different sequence evolution models, various indel distributions, basically everything you could wish for. As such the code is
Pitiful Bioinformatics MUMmer: The Pitiful State of Software Engineering in Bioinformatics MUMmer is one of the most used sequence alignment tools, right after BLAST. Most of its code base is quite old but still being actively developed (see MUMmer4). The following issue has been
Pitiful Bioinformatics The Pitiful State of Software Engineering in Bioinformatics This post will kick off a series of blog posts about the pitiful state of software engineering in bioinformatics. In each post I will take a stab at a popular tool in bioinformatics,
Errors in the Ensembl Genomes Database The Ensembl Bacteria database contains more than 2600 whole genomes sequences of Escherichia coli. It should not be a surprise that some of this data will be flawed. As a simple verification I
Avoid mutable by-value-capture in C++ Here is a quirks I stumbled upon in modern C++. As an example we will be printing all odd numbers in a vector and the count of odd number so far. For the
How to write a zsh completion zsh, an alternative to bash, is known for its superior completion system. This provides the user with a convenient way to input arguments and options to a command. It really is a time
Learning Perl in 2017 For a course on genetic analysis I was required to learn Perl (5). I now spend a week with two books and must say that not only did all my prejudices against Perl
Spielbericht E2 Die Einsiedlerin Die Einsiedlerin ist das zweite Abenteuer aus der Spielsteinkampagne für Das schwarze Auge. Nach etwa zweieinhalb Sitzung haben meine Spieler gestern das Tal wieder verlassen. Anbei ein Bericht, was mir an dem Abenteuer
The Missing Cow Call Linux allows users to allocate memory via mmap(2). This can then be shrunk, grown, and moved by mremap(2). The feature of the last syscall is that no data actually gets copied.
Bezahlter Inhalt Die Tage erreichte mich per Mail die folgende Anfrage (persönliche Daten redigiert). Hallo Fabian Kloetzl, für meine Kunden suche ich hochwertige Artikelplätze mit thematischem Bezug. Ein konkretes Interesse meines Kunden auf Ihrer Seite
A Compiler Bug Today, I was trying to validate some user input with C++11's new regular expressions. In essence, I tried the following. auto r = std::regex("[0\\- ]"); std::cout <<
dsa Tumult in Oberbüll Erst neulich ging das Scriptorium Aventuris online. Es erlaubt dem kreativen DSA-Fan seine eigenen Werke zum Download zur Verfügung zu stellen. Letzteres sogar gegen ein Entgelt. In diesem Post möchte ich mein Kurzabenteuer
dsa Fuzzy Logic im Rollenspiel Dies ist ein Post im Rahmen des Karnevals der Rollenspielblogs vom Oktober 2016 mit dem Thema Quellcode, Binärcode und Fuzzylogic. Was haben drei Begriffe aus der Informatik mit Rollenspiel zu tun? Eine ganze
z-push bei uberspace So richtig funktioniert das alles nicht. Hat jemand eine Idee, was ichvergessen habe? Mich störte schon länger, dass Mails auf meinem Desktop ankamen, bevor sie auf mein Telefon gepusht wurden. Dies konnte ich
Epson PULSENSE 20-0101-0008 To save battery life I disconnected my Epson PULSENSE watch from my phone for a few days. When I tried to reconnect, I always got the error 20-0101-0008. But finally I managed to
On Bootstrapping Whole Genomes Bootstrapping has been the de-facto standard for computing support-values of phylogenies for decades; and it has served us well. However, with the rise of high-throughput sequencing its limits became apparent. Not only is
The Fastest Way to Compute the Reverse Complement Bit-twiddling on genomes seems to become a regular pattern in this blog; See calculating the gc-content and hashing nucleotides. Today I will go into details on computing the reverse complement. Complementing Ever since
Beautiful Code In a recent TED Talk Linus Torvalds gave a simple example for beautiful code; the kind of code he aims for within Linux. It is the kind of code that everyone should strive
About const and kfree If you, like me, assumed that const in C relates to constant than this post will shock you. const will (at best) mean read-only; And if we talk about const-pointers even that is
Hashing Nucleotides to two Bits In many bioinformatics applications it is useful to reduce genomic sequences to 2bit format; Hash them, in some sense. Obviously two bits are enough to uniquely identify the four canonical bases. Usually the
Enabling TRIM for SSDs after installation Recently I reinstalled my Antergos (Arch Linux). It features a nice installer, Cnchi, with support for full disc encryption with LUKS and LVM. Unfortunately, it does not activate TRIM support for SSDs by