Java parser for BigWig ?

Question: Java parser for BigWig ?
2	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 ? bigwig wig format java	created 14 months ago by Pierre Lindenbaum ♦♦ 3514•3•27•68
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5	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	created 10 months ago by Jim Robinson 8•1
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	Many thanks Jim ! :-) log in to reply • written 10 months ago by Pierre Lindenbaum ♦♦ 3514•3•27•68

1	I would recommend contacting the IGV folks (igv-help (at) broadinstitute.org). Jim Robinson, the primary developer of IGV, will likely know.	created 14 months ago by Aaronquinlan ♦ 471•4•21
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	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. log in to reply • written 14 months ago by Pierre Lindenbaum ♦♦ 3514•3•27•68 1 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. log in to reply • written 13 months ago by Jim Robinson 8•1

2	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	created 11 months ago by Pierre Lindenbaum ♦♦ 3514•3•27•68
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	1 Excellent example for diving into JNI! log in to reply • written 11 months ago by Marcin Cieslik 48•3•7