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
