Package: fastqc / 0.11.5+dfsg-6
Metadata
Package | Version | Patches format |
---|---|---|
fastqc | 0.11.5+dfsg-6 | 3.0 (quilt) |
Patch series
view the series filePatch | File delta | Description |
---|---|---|
build_xml.patch | (download) |
build.xml |
8 5 + 3 - 0 ! |
use debian packaged jars |
fastqc.patch | (download) |
fastqc |
12 5 + 7 - 0 ! |
ensure proper classpath according to location of debian jars |
fix help call.patch | (download) |
uk/ac/babraham/FastQC/FastQCMenuBar.java |
2 1 + 1 - 0 ! |
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 |
set_configuration_path.patch | (download) |
uk/ac/babraham/FastQC/Modules/AdapterContent.java |
4 3 + 1 - 0 ! |
use config in debian etc dirs instead of embedding data in jar |
adapt_to_htslib.patch | (download) |
uk/ac/babraham/FastQC/Sequence/BAMFile.java |
13 7 + 6 - 0 ! |
path to samtools changed when switching from libsam-java to libhtsjdk-java |
drop fast5.patch | (download) |
fastqc |
11 0 + 11 - 0 ! |
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. |
htsjdk api.patch | (download) |
uk/ac/babraham/FastQC/Sequence/BAMFile.java |
16 9 + 7 - 0 ! |
use correct samreader api |