| Patch |
File delta |
Description |
| alter_pom_for_debian_packaging.patch | (download) |
pom.xml |
2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-) |
have good artifact name in pom.xml
We change the artifact name to snpeff to conform to Debian Java policy
for the name of the jar.
|
| update_launching_script_and_config_file_for_Debian.patch | (download) |
config/snpEff.config |
2 1 + 1 - 0 !
scripts/snpEff |
26 14 + 12 - 0 !
src/main/java/org/snpeff/PromoterSequences.java |
2 1 + 1 - 0 !
src/main/java/org/snpeff/SnpEff.java |
2 1 + 1 - 0 !
src/main/java/org/snpeff/snpEffect/Config.java |
21 20 + 1 - 0 !
src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdProtein.java |
2 1 + 1 - 0 !
src/main/java/org/snpeff/snpEffect/testCases/integration/CompareEffects.java |
6 3 + 3 - 0 !
src/main/java/org/snpeff/snpEffect/testCases/integration/CompareToEnsembl.java |
2 1 + 1 - 0 !
src/main/java/org/snpeff/snpEffect/testCases/integration/CreateSpliceSiteTestCase.java |
2 1 + 1 - 0 !
src/main/java/org/snpeff/snpEffect/testCases/integration/TestCasesHgvsBase.java |
2 1 + 1 - 0 !
src/main/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationBase.java |
10 5 + 5 - 0 !
src/main/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationExonFrame.java |
2 1 + 1 - 0 !
src/main/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationLof.java |
2 1 + 1 - 0 !
src/main/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationNmd.java |
2 1 + 1 - 0 !
src/main/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationVariant.java |
4 2 + 2 - 0 !
src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesBase.java |
2 1 + 1 - 0 !
src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesBaseApply.java |
2 1 + 1 - 0 !
src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesBuild.java |
4 2 + 2 - 0 !
18 files changed, 58 insertions(+), 37 deletions(-) |
alter the launching script, the config file and relevant java
files for a Debian install:
- Simplify the paths to account for a Debian installation.
- Use the default /etc/snpeff/snpEff.config file as configuration file if no
file was given in the command line: it will be copied into
~/.snpEff/snpEff.config, which will be used as the configuration file is no
other is given on the command line.
- By default, put data in ~/.snpEff/data.
- Correct bashisms in the launching script.
- In Config.java, use per-user config file if available. Else use the file in
/etc/snpeff. Else (which should normally just concern the unit tests), use
default file which should be in the source tree.
- Indicate path to effective config file in Java files.
|
| use_fastq_from_biojava6.patch | (download) |
pom.xml |
5 5 + 0 - 0 !
src/main/java/org/snpeff/Fastq2Fastq.java |
4 2 + 2 - 0 !
src/main/java/org/snpeff/Qseq2Fastq.java |
2 1 + 1 - 0 !
src/main/java/org/snpeff/binseq/DnaAndQualitySequence.java |
4 2 + 2 - 0 !
src/main/java/org/snpeff/binseq/DnaAndQualitySequenceWithId.java |
2 1 + 1 - 0 !
src/main/java/org/snpeff/fastq/FastqTools.java |
2 2 + 0 - 0 !
src/main/java/org/snpeff/fastq/FastqTrimmer.java |
3 3 + 0 - 0 !
src/main/java/org/snpeff/fastq/FastqTrimmerAdrian.java |
2 2 + 0 - 0 !
src/main/java/org/snpeff/fastq/FastqTrimmerMedian.java |
2 2 + 0 - 0 !
src/main/java/org/snpeff/fileIterator/FastqFileIterator.java |
6 3 + 3 - 0 !
src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesDnaOverlap.java |
2 1 + 1 - 0 !
src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesDnaSequence.java |
4 2 + 2 - 0 !
src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesSequenceIndexer.java |
4 2 + 2 - 0 !
src/main/java/org/snpeff/util/GprSeq.java |
4 2 + 2 - 0 !
14 files changed, 30 insertions(+), 16 deletions(-) |
using fastq* classes from biojava6-live
|
| omit_unused_junit_classes_and_integration_tests.patch | (download) |
pom.xml |
13 13 + 0 - 0 !
1 file changed, 13 insertions(+) |
compiling and running unit tests in the maven test step
No need to compile the tests during the compile step.
Not running integration tests.
|
| exclude_tests_with_missing_data.patch | (download) |
src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesCytoBands.java |
3 3 + 0 - 0 !
src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesGenomicSequences.java |
3 3 + 0 - 0 !
src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesNmers.java |
2 2 + 0 - 0 !
3 files changed, 8 insertions(+) |
skipping tests requiring non existing files
I guess such tests should rather be integration tests.
|
| lowering_heap_allocation.patch | (download) |
scripts/snpEff |
6 5 + 1 - 0 !
1 file changed, 5 insertions(+), 1 deletion(-) |
lowering heap allocation so that it passes on all supported
architectures; keeping it as is for 64-bit arches.
|
