Re: Help needed to update to latest fastqc
Hi Olivier,
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/libsis-base-java/
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/libsis-jhdf5-java/
I've not modified FastQC at all. Or rather, I tried patching out the
FAST5 support but I just did that within the vanilla source; I'm not
playing with the package from GIT at this point.
Cheers,
TIM
On Fri, 2015-08-14 at 08:16 +0200, olivier.sallou@codeless.fr wrote:
> On 08/13/2015 05:20 PM, Tim Booth wrote:
>
> > Hi Olivier,
> >
> > Looks like Bernd Rinn is making positive noises regarding a DFSG version
> > of the library, so hopefully once he provides code you can take what I
> > have done and make use of it. I committed to SVN because it's so much
> > easier than pushing to GIT and I'm lazy, sorry.
> what do you mean by commit to SVN ?
>
> I looked at SVN repo for fastqc but it is empty, referring to git repo
> [0]
> Where is you code ?
>
> [0] http://anonscm.debian.org/viewvc/debian-med/trunk/packages/fastqc/
>
> Olivier
> >
> > In my libsis-jhdf5-java package I created a small test
> > "ReadWriteTest.java" which I confirmed works correctly when used with
> > the binary libhdf5.so supplied by upstream. Also my patches
> > fix_dodgy_cast.patch and remove_ch_rinn_imports.patch should be sound
> > but the others are junk caused by me trying to kick the code into
> > submission.
> >
> > If for some reason we can't get this working then you could very easily
> > patch out FAST5 support in FastQC for now. My impression is that it's
> > something of an alpha feature in any case. I can't even find a .fast5
> > format file to test with!
> >
> > > > > PATCH for FASTQC
> > This patch disables support for FAST5 format until we get the library built.
> > Most users won't need this anyway, and those that do can convert the file
> > to FASTQ using other tools.
> >
> > Note you also need to completely remove the file
> > uk/ac/babraham/FastQC/Sequence/Fast5File.java, which I can't do in a quilt patch.
> >
> > Tim Booth - 13th Aug 2015
> > --- a/uk/ac/babraham/FastQC/Sequence/SequenceFactory.java
> > +++ b/uk/ac/babraham/FastQC/Sequence/SequenceFactory.java
> > @@ -100,7 +100,8 @@
> > return new BAMFile(file,false);
> > }
> > else if (file.getName().toLowerCase().endsWith(".fast5")) {
> > - return new Fast5File(file);
> > + //return new Fast5File(file);
> > + throw new SequenceFormatException("Support for FAST5 files has not been enabled in this build of FastQC.");
> > }
> > else {
> > return new FastQFile(config,file);
> > <<<PATCH
> >
> > I'm done with this for now. Off to debug some Python code.
> >
> > Best,
> >
> > TIM
> >
>
>
> --
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--
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