I am starting csid base packaging from your work. I could build native libs,
adding some autotools script to avoid using upstream scripts (one per arch).
I am adding auto test to check cisd java with native libs. Still need some
patching.
I am quite confident to get package soon. Once ready i will look at jhfd5
package. I won t focus immediatly on polishing ( control desc ...).
Oliviet
Envoyé depuis mon smartphone Sony Xperia™ via le réseau SFR
---- Tim Booth a écrit ----
>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.
>
>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
>
