Java Parser For Bigwig ?

Question

[Pierre Lindenbaum]

Hi all,

In the following paper:

BigWig and BigBed: enabling browsing of large distributed datasets. Kent & al. Bioinformatics (2010) 26 (17): 2204-2207. ( http://bioinformatics.oxfordjournals.org/content/26/17/2204.full )

it is said:

... a Java implementation in progress (Martin Deacutis, personal communication) for use in the Integrative Genome Viewer (http://www.broadinstitute.org/igv/).

I can't find Dr Deacutis's mail. Does anyone knows if this library has been implemented somewhere ?

Answer 1

[Jim Robinson]

And at long last the IGV BigWig/BigBed code is finished. I've carved it out as a stand-alone project, which you can access at http://code.google.com/p/bigwig. To see it in action in a Java client download IGV from http://www.broadinstitute.org/igv and load a bigwig or bigbed file (extensions bw, bigwig, bb, or bigbed). You can load by URL or from a file.

Jim

[Pierre Lindenbaum]

Many thanks Jim ! :-)

Answer 2

[Pierre Lindenbaum]

I've just written a java JNI interface using Jim Kent's C API for BigWig.

See my blog:

"Handling a BigWig file from Java+JNI : my notebook " http://plindenbaum.blogspot.com/2011/06/handling-bigwig-file-from-javajni-my.html

[Marcin Cieslik]

Excellent example for diving into JNI!

Answer 3

[Aaronquinlan]

I would recommend contacting the IGV folks (igv-help (at) broadinstitute.org). Jim Robinson, the primary developer of IGV, will likely know.

[Jim Robinson]

Yes, the repository is at http://code.google.com/p/bigwig/. I actually think the code is complete, Marty tested it on some some files before he left. All that is needed (hopefully) is some testing.

[Pierre Lindenbaum]

Jim Robinson said that Dr Deacutis left the Broad Inst. before finishing this work. He said he would put the current sources in a (public?) repository.