Re: Help needed to update to latest fastqc

["olivier.sallou@codeless.fr" <olivier.sallou@codeless.fr>]

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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