ascii-alignment-pileup merge requestshttps://git.scicore.unibas.ch/zavolan_group/tools/ascii-alignment-pileup/-/merge_requests2024-01-22T14:51:45Zhttps://git.scicore.unibas.ch/zavolan_group/tools/ascii-alignment-pileup/-/merge_requests/10feat: add output prefix assignment2024-01-22T14:51:45ZIris Mestres Pascualfeat: add output prefix assignmentThis PR closes #2 .
In order to allow the assignment of the prefix to be made without changing the current behavior, a new CLI argument (`--prefix`) has been added and set by default to an empty string.
During the prefix assignment, if...This PR closes #2 .
In order to allow the assignment of the prefix to be made without changing the current behavior, a new CLI argument (`--prefix`) has been added and set by default to an empty string.
During the prefix assignment, if the user has not provided a prefix, the input BAM file name(s) is used instead.Iris Mestres PascualIris Mestres Pascualhttps://git.scicore.unibas.ch/zavolan_group/tools/ascii-alignment-pileup/-/merge_requests/9fix: ref does not match pileups in example2023-02-20T01:03:20ZAlex Kanitzfix: ref does not match pileups in example* Reference sequence in tests did not match the corresponding alignments, region and miRNA annotation files.
* Update reference sequence, BGZIPped version, test output file and md5 sum of test output file
* Add `tabix` dependency to gene...* Reference sequence in tests did not match the corresponding alignments, region and miRNA annotation files.
* Update reference sequence, BGZIPped version, test output file and md5 sum of test output file
* Add `tabix` dependency to generate BGZIPped reference to Conda environment file
* Update documentation
* No update to codehttps://git.scicore.unibas.ch/zavolan_group/tools/ascii-alignment-pileup/-/merge_requests/8ci: automatically add release2022-07-10T14:20:44ZAlex Kanitzci: automatically add releaseAlex KanitzAlex Kanitzhttps://git.scicore.unibas.ch/zavolan_group/tools/ascii-alignment-pileup/-/merge_requests/7ci: add Conda tests and refactor2022-07-10T13:21:07ZAlex Kanitzci: add Conda tests and refactorAlex KanitzAlex Kanitzhttps://git.scicore.unibas.ch/zavolan_group/tools/ascii-alignment-pileup/-/merge_requests/6build: add Conda environment specification2022-07-10T11:55:56ZAlex Kanitzbuild: add Conda environment specificationAlex KanitzAlex Kanitzhttps://git.scicore.unibas.ch/zavolan_group/tools/ascii-alignment-pileup/-/merge_requests/5ci: add GitLab CI config2022-07-10T11:26:05ZAlex Kanitzci: add GitLab CI configAlex KanitzAlex Kanitzhttps://git.scicore.unibas.ch/zavolan_group/tools/ascii-alignment-pileup/-/merge_requests/4test: include reference file2022-07-10T09:26:47ZAlex Kanitztest: include reference fileAlex KanitzAlex Kanitzhttps://git.scicore.unibas.ch/zavolan_group/tools/ascii-alignment-pileup/-/merge_requests/3test: add test files and docs2022-07-09T08:21:01ZAlex Kanitztest: add test files and docsAlex KanitzAlex Kanitzhttps://git.scicore.unibas.ch/zavolan_group/tools/ascii-alignment-pileup/-/merge_requests/2build: add Dockerfile2022-07-09T07:54:55ZAlex Kanitzbuild: add DockerfileAlex KanitzAlex Kanitzhttps://git.scicore.unibas.ch/zavolan_group/tools/ascii-alignment-pileup/-/merge_requests/1docs: add README.md2022-07-09T06:48:23ZAlex Kanitzdocs: add README.mdAlex KanitzAlex Kanitz