[Gmod-ajax] Please test JBrowse git master

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[Gmod-ajax] Please test JBrowse git master

Mitch Skinner
Thanks for all the bug reports; several of them should be fixed in the
HEAD version of the JBrowse master branch now.

Specifically, this should address:

Gregg's two reports, the segfault and the error message from Storable
about storing CODE items.  The segfault wasn't technically a JBrowse
bug, but JBrowse now avoids doing the thing that triggers the bug.

Brenton's first report about "cmp" not being implemented on
Bio::Annotation::SimpleValue.  I haven't seen that error myself, but I
fixed what I believe to be the problem; please test.

Chris' report about biodb-to-json.pl being slow.  With my test data set
(smaller than Chris'), on one track that I've been benchmarking, doing
one refseq took 34 seconds with JBrowse 1.1, 148 seconds with JBrowse
1.2, and 39 seconds with git HEAD.

We're still looking at the other reports, including Brenton's one about
wig-to-json.pl being much slower.

Mitch



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Re: Please test JBrowse git master

Gregg Helt
Trying now with JBrowse master HEAD.  Preliminary testing with refseq
bed file, flatfile-to-json.pl is working well.

Thanks Mitch!

Gregg

On Sat, Feb 26, 2011 at 4:30 AM, Mitch Skinner
<[hidden email]> wrote:

> Thanks for all the bug reports; several of them should be fixed in the HEAD
> version of the JBrowse master branch now.
>
> Specifically, this should address:
>
> Gregg's two reports, the segfault and the error message from Storable about
> storing CODE items.  The segfault wasn't technically a JBrowse bug, but
> JBrowse now avoids doing the thing that triggers the bug.
>
> Brenton's first report about "cmp" not being implemented on
> Bio::Annotation::SimpleValue.  I haven't seen that error myself, but I fixed
> what I believe to be the problem; please test.
>
> Chris' report about biodb-to-json.pl being slow.  With my test data set
> (smaller than Chris'), on one track that I've been benchmarking, doing one
> refseq took 34 seconds with JBrowse 1.1, 148 seconds with JBrowse 1.2, and
> 39 seconds with git HEAD.
>
> We're still looking at the other reports, including Brenton's one about
> wig-to-json.pl being much slower.
>
> Mitch
>
>
>

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insights. http://p.sf.net/sfu/splunk-dev2dev 
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