| Patch |
File delta |
Description |
| class path.patch | (download) |
Makefile |
4 3 + 1 - 0 !
1 file changed, 3 insertions(+), 1 deletion(-) |
look for jars in /usr/share/java rather than ./lib
The bundled jar files in lib/ have been removed for Debian, so the
build system ought to find the packaged versions in /usr/share/java.
This patch allows overriding the CLASSPATH while calling make. This
way, we can change it from within debian/rules.
|
| jar rules.patch | (download) |
Makefile |
32 5 + 27 - 0 !
1 file changed, 5 insertions(+), 27 deletions(-) |
leave out removed files when building jar files
The recipe to build the jar files looks for some files
that have been excluded from the source distribution (lib/*).
Their absence causes "can not stat" errors, so any reference to
them is removed here.
|
| test classpath.patch | (download) |
test/build-test.xml |
12 2 + 10 - 0 !
1 file changed, 2 insertions(+), 10 deletions(-) |
change classpath to use external jars in build-test.xml
|
| picard api change.patch | (download) |
uk/ac/sanger/artemis/components/alignment/BamUtils.java |
8 4 + 4 - 0 !
uk/ac/sanger/artemis/components/alignment/BamView.java |
32 16 + 16 - 0 !
uk/ac/sanger/artemis/components/alignment/BamViewRecord.java |
2 1 + 1 - 0 !
uk/ac/sanger/artemis/components/alignment/CRAMReferenceSequenceFile.java |
6 3 + 3 - 0 !
uk/ac/sanger/artemis/components/alignment/CoveragePanel.java |
4 2 + 2 - 0 !
uk/ac/sanger/artemis/components/alignment/PairedReadComparator.java |
2 1 + 1 - 0 !
uk/ac/sanger/artemis/components/alignment/ReadGroupsFrame.java |
2 1 + 1 - 0 !
uk/ac/sanger/artemis/components/alignment/RunSamTools.java |
2 1 + 1 - 0 !
uk/ac/sanger/artemis/components/alignment/SAMRecordFlagConjunctionPredicate.java |
2 1 + 1 - 0 !
uk/ac/sanger/artemis/components/alignment/SAMRecordFlagPredicate.java |
2 1 + 1 - 0 !
uk/ac/sanger/artemis/components/alignment/SAMRecordList.java |
2 1 + 1 - 0 !
uk/ac/sanger/artemis/components/alignment/SAMRecordMapQPredicate.java |
2 1 + 1 - 0 !
uk/ac/sanger/artemis/components/alignment/SAMRecordPositionComparator.java |
2 1 + 1 - 0 !
uk/ac/sanger/artemis/components/alignment/SAMRecordPredicate.java |
2 1 + 1 - 0 !
uk/ac/sanger/artemis/components/alignment/SnpPanel.java |
4 2 + 2 - 0 !
uk/ac/sanger/artemis/components/variant/BCFReader.java |
2 1 + 1 - 0 !
uk/ac/sanger/artemis/components/variant/IOUtils.java |
2 1 + 1 - 0 !
uk/ac/sanger/artemis/components/variant/TabixReader.java |
4 2 + 2 - 0 !
uk/ac/sanger/artemis/components/variant/VCFview.java |
2 1 + 1 - 0 !
uk/ac/sanger/artemis/io/DocumentEntryFactory.java |
2 1 + 1 - 0 !
uk/ac/sanger/artemis/io/IndexFastaStream.java |
10 5 + 5 - 0 !
uk/ac/sanger/artemis/io/IndexedGFFDocumentEntry.java |
2 1 + 1 - 0 !
uk/ac/sanger/artemis/plot/UserDataAlgorithm.java |
2 1 + 1 - 0 !
uk/ac/sanger/artemis/util/FTPSeekableStream.java |
2 1 + 1 - 0 !
uk/ac/sanger/artemis/util/FileDocument.java |
4 2 + 2 - 0 !
25 files changed, 53 insertions(+), 53 deletions(-) |
use htsjdk for dropped picard and sam functionality
|
| htsjdk api change.patch | (download) |
uk/ac/sanger/artemis/components/alignment/BamView.java |
2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-) |
adjust log configuration to new api
|
| samreader.patch | (download) |
uk/ac/sanger/artemis/components/alignment/BamUtils.java |
56 28 + 28 - 0 !
uk/ac/sanger/artemis/components/alignment/BamView.java |
1108 555 + 553 - 0 !
2 files changed, 583 insertions(+), 581 deletions(-) |
implement new htsjdk api
See https://github.com/samtools/htsjdk/issues/767#issuecomment-264864910
|
| use lang3.patch | (download) |
uk/ac/sanger/artemis/io/GFF3Encoder.java |
2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-) |
use lang3
|
