25 January 2013

Samtools tview as a library to display the BAM

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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...
3 comments:
09 January 2013

A XML schema (xsd) for GeneOntology

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The GeneOntology can be downloaded as a RDF/XML file from http://archive.geneontology.org/latest-termdb/go_daily-termdb.rdf-xml.gz . Althou...
20 December 2012

RDF/Jena: a simple extension for XSLT/XALAN. Testing with NCBI-Gene

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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 ...
29 November 2012

Reading/Writing a VCF file with the GATK-API.

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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...
21 November 2012

visualizing the dependencies in a Makefile

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Update 2014: I wrote a C version at https://github.com/lindenb/makefile2graph . I've just coded a tool to visualize the dependencies in...
13 November 2012

Creating a virtual RDF graph describing a set of OpenOffice spreadsheets with Apache Jena and Fuseki

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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...
02 November 2012

Saving your tweets in a database using sqlite, rhino, scribe, javascript

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In the current post, I 'll describe a simple method to save your tweets in a sqlite database using Mozilla Rhino . Prerequisites sqlite...
15 October 2012

Modifying the GATK so it supports a XML-based format for VCF.

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I've modified the sources of the GATK in order to support a XML-based format for the variation in addition of the VCF format. Here are...