Debian Patches

Status for fastqc/0.11.9+dfsg-6

Patch	Description	Author	Forwarded	Bugs	Last update
htsjdk-api.patch	use correct SamReader API	Sascha Steinbiss <[email protected]>	no
build_xml.patch	Use Debian packaged JARs	Andreas Tille <[email protected]>	no		2015-12-04
fastqc.patch	Ensure proper CLASSPATH according to location of Debian JARs ===================================================================	Steffen Moeller <[email protected]>	no
fix-help-call.patch	The original way to open Help text ends up in an exception Setting the explicit 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	Andreas Tille <[email protected]>	no
set_configuration_path.patch	use config in Debian etc dirs instead of embedding data in jar	Olivier Sallou <[email protected]>	no
adapt_to_htslib.patch	Path to samtools changed when switching from libsam-java to libhtsjdk-java	Andreas Tille <[email protected]>	no	debian	2016-01-14
java-9.patch	Set Java 9 as build target No idea whether this has some influence finally but trying to get rid of this warning [javac] Using javac -source 1.5 is no longer supported, switching to 1.7 [javac] Using javac -target 1.5 is no longer supported, switching to 1.7 is intended by this patch.	Andreas Tille <[email protected]>	no		2018-04-27