build.xml | 8 5 + 3 - 0 !
1 file changed, 5 insertions(+), 3 deletions(-)

 use debian packaged jars

fastqc | 12 5 + 7 - 0 !
1 file changed, 5 insertions(+), 7 deletions(-)

 ensure proper classpath according to location of debian jars

uk/ac/babraham/FastQC/FastQCMenuBar.java | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 the original way to open help text ends up in an exception
 Setting the explicite file name as well as avoiding the call to
   ClassLoader.getSystemResource
 helps fixing this.  Specifically the later is important, see
   https://lists.debian.org/debian-med/2012/11/msg00073.html

uk/ac/babraham/FastQC/Modules/AdapterContent.java | 4 3 + 1 - 0 !
uk/ac/babraham/FastQC/Modules/ModuleConfig.java | 4 3 + 1 - 0 !
uk/ac/babraham/FastQC/Sequence/Contaminant/ContaminentFinder.java | 7 5 + 2 - 0 !
3 files changed, 11 insertions(+), 4 deletions(-)

 use config in debian etc dirs instead of embedding data in jar

uk/ac/babraham/FastQC/Sequence/BAMFile.java | 13 7 + 6 - 0 !
1 file changed, 7 insertions(+), 6 deletions(-)

 path to samtools changed when switching from libsam-java
 to libhtsjdk-java

fastqc | 11 0 + 11 - 0 !
uk/ac/babraham/FastQC/Sequence/Fast5File.java | 89 0 + 89 - 0 !
uk/ac/babraham/FastQC/Sequence/SequenceFactory.java | 3 0 + 3 - 0 !
3 files changed, 103 deletions(-)

 hdf5 1.10 is about to transition into unstable, and unfortunately
 a FastQC build-dependency, libsis-jhdf5-java, doesn't support this new
 release yet, and we have no information about its upstream schedule
 wrt HDF5 1.10.
 .
 libsis-jhdf5-java is required only to support fast5 files from nanopore
 sequences.
 .
 Since these files can easily be converted to FastQ format using
 poretools, I propose to temporarily drop fast5 support from FastQC
 to avoid a removal from testing.

uk/ac/babraham/FastQC/Sequence/BAMFile.java | 16 9 + 7 - 0 !
1 file changed, 9 insertions(+), 7 deletions(-)

 use correct samreader api