Andreas Tille pushed to branch upstream at Debian Med / paleomix
Commits: 48ed3c7f by Andreas Tille at 2018-12-17T11:09:15Z New upstream version 1.2.13.3 - - - - - 5 changed files: - CHANGES.md - README.rst - docs/bam_pipeline/configuration.rst - paleomix/__init__.py - paleomix/nodes/validation.py Changes: ===================================== CHANGES.md ===================================== @@ -1,5 +1,11 @@ # Changelog +## [1.2.13.3] - 2018-11-01 +### Fixed + - Fixed validation/read counting of pre-trimmed reads not including + the mate 1 files of paired-end reads. This resulted in the + 'seq_retained_reads' count being half the expected value. + ## [1.2.13.2] - 2018-04-22 ### Fixed @@ -575,8 +581,9 @@ the (partially) updated documentation now hosted on ReadTheDocs. - Switching to more traditional version-number tracking. -[Unreleased]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.2...HEAD -[1.2.13.1]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.1...v1.2.13.2 +[Unreleased]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.3...HEAD +[1.2.13.3]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.2...v1.2.13.3 +[1.2.13.2]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.1...v1.2.13.2 [1.2.13.1]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.13...v1.2.13.1 [1.2.13]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.12...v1.2.13 [1.2.12]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.11...v1.2.12 ===================================== README.rst ===================================== @@ -14,4 +14,4 @@ The PALEOMIX pipelines have been published in Nature Protocols; if you make use The Zonkey pipeline has been published in Journal of Archaeological Science; if you make use of this pipeline in your work, then please cite - Schubert M, Mashkour M, Gaunitz C, Fages A, Seguin-Orlando A, Sheikhi S, Alfarhan AH, Alquraishi SA, Al-Rasheid KAS, Chuang R, Ermini L, Gamba C, Weinstock J, Vedat O, and Orlando L. "**Zonkey: A simple, accurate and sensitive pipeline to genetically identify equine F1-hybrids in archaeological assemblages**". Journal of Archaeological Science. 2007 Feb; 78:147-157. doi: `10.1016/j.jas.2016.12.005 <http://dx.doi.org/10.1016/j.jas.2016.12.005>`_. + Schubert M, Mashkour M, Gaunitz C, Fages A, Seguin-Orlando A, Sheikhi S, Alfarhan AH, Alquraishi SA, Al-Rasheid KAS, Chuang R, Ermini L, Gamba C, Weinstock J, Vedat O, and Orlando L. "**Zonkey: A simple, accurate and sensitive pipeline to genetically identify equine F1-hybrids in archaeological assemblages**". Journal of Archaeological Science. 2017 Feb; 78:147-157. doi: `10.1016/j.jas.2016.12.005 <http://dx.doi.org/10.1016/j.jas.2016.12.005>`_. ===================================== docs/bam_pipeline/configuration.rst ===================================== @@ -9,7 +9,7 @@ The BAM pipeline exposes a number options, including the maximum number of threa .. code-block:: bash - $ paleomix bam_pipeline --write-config + $ paleomix bam_pipeline run --write-config The resulting file contains a list of options which can be overwritten:: ===================================== paleomix/__init__.py ===================================== @@ -21,7 +21,7 @@ # SOFTWARE. # -__version_info__ = (1, 2, 13, 2) +__version_info__ = (1, 2, 13, 3) __version__ = '%i.%i.%i.%i' % __version_info__ ===================================== paleomix/nodes/validation.py ===================================== @@ -112,10 +112,10 @@ class ValidateFASTQFilesNode(Node): self._files = set() for (read_type, filename) in input_files.iteritems(): if read_type == "Paired": - filename = filename.format(Pair=1) - filename = filename.format(Pair=2) - - self._files.add((read_type, filename)) + self._files.add((read_type, filename.format(Pair=1))) + self._files.add((read_type, filename.format(Pair=2))) + else: + self._files.add((read_type, filename)) input_files = [filename for _, filename in self._files] Node.__init__(self, View it on GitLab: https://salsa.debian.org/med-team/paleomix/commit/48ed3c7fbfedc936cbd51e706c598de19dc7d6d9 -- View it on GitLab: https://salsa.debian.org/med-team/paleomix/commit/48ed3c7fbfedc936cbd51e706c598de19dc7d6d9 You're receiving this email because of your account on salsa.debian.org.
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