Debian Patches

Status for snpeff/5.2.f+dfsg-1

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 <[email protected]> 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 <[email protected]> not-needed 2022-02-07
use_fastq_from_biojava6.patch Using Fastq* classes from biojava6-live Pierre Gruet <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> not-needed 2023-01-20

All known versions for source package 'snpeff'

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