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.sal...@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 > > > > > -- > gpg key id: 4096R/326D8438 (keyring.debian.org) > Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- Nothing is inherently mysterious - nothing that actually exists, that is. If I am ignorant about a phenomenon, that is a fact about my state of mind, not a fact about the phenomenon; to worship a phenomenon because it seems so wonderfully mysterious, is to worship your own ignorance. - Eliezer Yudkowsky