YOKOFAKUN

Here are four java-bases tools I wrote today for @SolenaLS to annotate VCF files. VCFTabix VCFTabix : we want to use the VCF of the 1K...

In the current post, I'll describe my first Open MPI program. Open MPI is "a Message Passing Interface (MPI) library, a standard...

Following that thread on Biostar , I've created a tool that compares two or more BAMs . This java program uses the Picard and berkeleyd...

Many tools in the Picard package produce some "Metrics File" (described at http://picard.sourceforge.net/picard-metric-definiti...

I've forked samtools and modified the code of tview to use it as a library to display the alignments. The original code is an inreracti...

The GeneOntology can be downloaded as a RDF/XML file from http://archive.geneontology.org/latest-termdb/go_daily-termdb.rdf-xml.gz . Althou...

In a previous post , I've shown that the XALAN XSLT engine can be extended with custom function returning a DOM Document that will be ...

This is a simple post to save my notes about reading a VCF file and writing it to another file using the java libraries of the GATK . The on...

Update 2014: I wrote a C version at https://github.com/lindenb/makefile2graph . I've just coded a tool to visualize the dependencies in...

In the current post, I will use the Jena API for RDF to implement a virtual RDF graph describing the content of a set of openoffice/libre...