| Patch | Description | Author | Forwarded | Bugs | Origin | Last update |
|---|---|---|---|---|---|---|
| protoc.patch | Using Debian-packaged protoc compiler | Pierre Gruet <pgt@debian.org> | not-needed | 2020-08-24 | ||
| adding_dependencies.patch | Adding missing dependencies to the various pom.xml files | Pierre Gruet <pgt@debian.org> | yes | 2020-10-31 | ||
| using_jbzip2.patch | using the classes of libjbzip2-java as a replacement for Bzip2* | Pierre Gruet <pgt@debian.org> | not-needed | 2021-08-04 | ||
| adapting_to_old_fastutil.patch | changing some imports linked to fastutil classes Goby 3.3.1 was written for an old fastutil library. | Pierre Gruet <pgt@debian.org> | not-needed | 2021-08-04 | ||
| using_GeneratedMessageV3.patch | using GeneratedMessageV3 from protobuf to replace GeneratedMessage The protobuf package has changed quite a bit since the version goby 3.3.1 relies on was edited. |
Pierre Gruet <pgt@debian.org> | not-needed | 2021-08-04 | ||
| using_commons-cli.patch | using classes of commons-cli instead of unpackaged ones | Pierre Gruet <pgt@debian.org> | not-needed | 2021-07-31 | ||
| using_correct_SamReader_api.patch | using the correct SamReader api | Pierre Gruet <pgt@debian.org> | not-needed | https://sources.debian.org/src/fastqc/0.11.9+dfsg-4/debian/patches/htsjdk-api.patch | 2020-11-06 | |
| inclusions_in_SplitTranscriptsMode.patch | reading class GeneTranscriptRelationships from Goby archive The above-named class is in the archive of Goby and thus does not need to be read elsewhere. | Pierre Gruet <pgt@debian.org> | yes | 2020-11-02 | ||
| catch_IOException_LineIterator.patch | Catch the IOException launched by close() method of LineIterator | Pierre Gruet <pgt@debian.org> | yes | 2020-11-03 | ||
| computing_fisher_pvalue_hypergeom.patch | computing p-values by hand as gominer is not packaged in Debian | Pierre Gruet <pgt@debian.org> | yes | 2021-08-05 | ||
| exclude_not_runnable_tests.patch | modify a few tests when requiring unpackaged tools junitx.framework is not packaged, the test files TestSplicedSamHelper.java and TestAlignmentReader.java, that use it, are deactivated in goby-distribution/pom.xml. We also exclude TestGobyPaperTop5000s.java in this pom, as data files that it uses are not provided in the source. Two tests in TestSamRecordParser are skipped for the same reason. One test in TestConcatAlignmentReader needs a file that does not exist. The tests in TestIterateSortedAlignment all use a file that does not exist. One test in TestSkipTo needs to use the network. One test in TestStatistics is skipped as it expects a Fisher test p-value greater than 0.05, which seems false after a check with R and also with a script using libdistlib-java. Tests in TestDiscoverSequenceVariantsIndelGenotypes and in TestDiscoverSequenceVariantsMode need genotype.jar or somatic.jar, which are not in this package nor in a dependency. . Also I removed some tests that fail even in a classic Maven build. Maybe this is wrong, but anyway they are not run in the classic Maven build and so I am unsure upstream has kept them up to date. I opened an issue at the link below. Ignored tests are: - three tests in TestConcatSortedAlignmentReader; - all tests in TestIteratedSortedAlignment2; - one test in TestRealignmentProcessor; - all tests in TestDiscoverSVMethylationRatesMode; - five tests in TestDiscoverSequenceVariantsMode; - three tests in TestLastToCompact; - one test in TestReformatCompactReadsMode; - one test in TestSortMode; - two tests in TestCompareGroupsVCFOutputFormat; - two tests in MergeIndelFromTest. . Finally, I removed the tests - in ConcatenateAlignmentModeTest.java (one test); - HTSJDKReaderImplTest.testReadingBAM; - HTSJDKReaderImplTest.testWithPosition; - HTSJDKReaderImplTest.testWithSlices; - TestConcatAlignmentReader.testConcatSamBam which succeed, but need a lot of large data files which I removed when repacking. |
Pierre Gruet <pgt@debian.org> | yes | 2021-08-18 | ||
| goby_script.patch | modifying the launcher script to account for Debian paths | Pierre Gruet <pgt@debian.org> | not-needed | 2021-08-08 | ||
| path_of_goby_jar_for_Debian.patch | ensuring the correct Debian path of the goby jar will show up This is important for usage messages that are printed when the user invokes goby with --help. |
Pierre Gruet <pgt@debian.org> | not-needed | 2021-08-08 | ||
| jaxb_dependency.patch | adding missing jaxb-api dependency in pom | Pierre Gruet <pgt@debian.org> | yes | 2021-11-23 | ||
| using_pcre2.patch | switching from pcre3 to pcre2 This was tested by running pcreTest (in cpp/src/GsnapParseTest1.cc) successfully. Yet I did not compile the other files. |
Pierre Gruet <pgt@debian.org> | yes | debian | 2021-11-26 | |
| omit_test_failing_randomly.patch | omit tests that fail randomly | Pierre Gruet <pgt@debian.org> | yes | 2022-07-03 | ||
| adding_opens_arg_for_tests.patch | adding a --add-opens argument needed to run the tests, starting from OpenJDK17. | Pierre Gruet <pgt@debian.org> | no | 2022-11-18 |