29 May 2013

Binding a C library with Javascript/ #mozilla. An example with the Tabix library

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In this post I'll show how to bind a C API to javascript using the mozilla/xul-runner API and the tabix library. About xpcshell XULR...
26 May 2013

Filtering a VCF with javascript

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This is my answer for that question on biostar . I wrote a java program filtering the VCF with the rhino javascript-engine. I put the cod...
1 comment:
24 May 2013

A Tribble/FeatureCodec handling JSON-based annotations files.

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I wrote a java FeatureCodec for JSON with a the tribble library. Citing the GATK tream: "The Tribble project was started as an effor...
22 May 2013

Drawing a Timeline with jquery.

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In 2008, I wrote a XUL -based interface displaying a timeline ( http://...freebase-and-history-of-sciences.html ). Here I've played wi...
15 May 2013

VIZBAM and NGSProject

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FYI: I've started the following projects on github: VizBam Vizbam ( https://github.com/lindenb/vizbam ) is a java library used to di...
01 May 2013

Inserting the result of a BLAST into a Database using XSLT.

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Here is the XML output of a BLAST: <?xml version="1.0"?> <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN...
26 April 2013

Java JNI bindings for BWA(mem-lite)

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Motivation BWA 7.4( http://bio-bwa.sourceforge.net/ ) contains a small C example( https://github.com/lh3/bwa/blob/master/example.c ) for r...
4 comments:
23 April 2013

playing with BWA-MEM : my notebook

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BWA-MEM , is a new tool that is part of the latest version of BWA . As said Heng Li on Biostar bwa-mem can be used to identify the viral in...
25 March 2013

Embedding Pubmed, Graphiviz and a remote image in #LaTeX. My notebook. .

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I'm learning LaTeX . Today I learned how to create a new command in LaTeX. \newcommand{name}[num]{definition} "Basically the comm...
1 comment:
13 March 2013

Filtering a BAM with javascript.

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The following was created to answer that question on biostar: " Exclude reads with XA tag ". SamJs is a java program filtering th...