The Polynerd

Revcomp – Part 2: The Table

In part one we used a switch statement to find the complement of a given base. Note how the nucleotides in the code are arranged in what looks like a table. However, this table is laid out in instructions space. Let's convert it to

Bioinformatics

On Computing the Reverse Complement

When Watson and Crick described the two-stranded structure of DNA they stated that "if the sequence of bases on one chain is given, then the sequence on the other chain is automatically determined." This observation is crucial to much modern biology such as sequencing

Bioinformatics

PFASTA — Yet another set of FASTA tools

Recently more and more CVEs are being filed against bioinformatic tools. Validity of the bug reports aside, it just shows that the security aspects of scientific software becomes more interesting. One of the most important factors is parsing and validating input data. Correctly handling

Bioinformatics

Optimizing Mash

Mash could well be the new BLAST. It is a great technique to compute similarity scores for sequences. However, its implementation is not optimal. In this blog post I describe some tricks to increase the performance substantially. Addendum: Some people find this blog post

Bioinformatics

Static Libraries

Parsing a FASTA file or any file format can be hard. But mostly writing a parser can be cumbersome. Thus, people don't do it properly or just copy someone elses work. For reading FASTA files a lot of bioinformatics tools use kseq.h. However,

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 it is of interest to find and mark the violating evidence.

Bioinformatics

strlen(genome)

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 quirks of C. Strings in C are null-terminated and their length

Bioinformatics

FASTA

“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 by humans. However, the lack of a formal specification leads to

Bioinformatics

RSPR

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 authors decided not to use a standard way for parsing commandline

Bioinformatics

INDELible

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 pretty massive. It is also quite messy. The worst part: It

Bioinformatics

MUMmer

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 sitting in there for over five years. struct Score { long int

Bioinformatics

The State of Software Engineering in Bioinformatics

This post will kick off a series of blog posts about the state of software engineering in bioinformatics. In each post I will take a stab at a popular tool in bioinformatics, dive in its code and show some of its worst parts. The

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 took my own tool for phylogenetic reconstruction, andi, and applied it

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 sake of demonstration I'll be using the following method. #include <

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 saver and more tools should come with a completion script. For

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 come true, it is even worse than I imagined. Where all

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

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. Instead the physical memory pages are simply mapped to different virtual

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 zu buchen besteht bereits. So bin ich auf Ihre Seite aufmerksam

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 << std::regex_match(some_string, r) << std::endl; The

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 Tumult in Oberbüll vorstellen. Seid gewarnt vor Spoilern. Nicht unweit der

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

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 nun durch den Einsatz von z-push fixen. Dabei habe ich mich

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 do it, here is the trick; disconnect completely: Tell your watch

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 it slow, but also the results become less useful, as the