| Patch | Description | Author | Forwarded | Bugs | Origin | Last update |
|---|---|---|---|---|---|---|
| alter_pom_for_debian_packaging.patch | 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. |
Pierre Gruet <pgt@debian.org> | not-needed | 2022-01-23 | ||
| update_launching_script_and_config_file_for_Debian.patch | 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. |
Pierre Gruet <pgt@debian.org> | not-needed | 2022-02-07 | ||
| use_fastq_from_biojava6.patch | Using Fastq* classes from biojava6-live | Pierre Gruet <pgt@debian.org> | not-needed | 2023-01-12 | ||
| omit_unused_junit_classes_and_integration_tests.patch | compiling and running unit tests in the Maven test step No need to compile the tests during the compile step. Not running integration tests. |
Pierre Gruet <pgt@debian.org> | not-needed | 2022-01-29 | ||
| exclude_tests_with_missing_data.patch | skipping tests requiring non existing files I guess such tests should rather be integration tests. | Pierre Gruet <pgt@debian.org> | not-needed | 2022-01-29 | ||
| lowering_heap_allocation.patch | lowering heap allocation so that it passes on all supported architectures; keeping it as is for 64-bit arches. | Pierre Gruet <pgt@debian.org> | not-needed | 2023-01-20 |