Commit 48ed3c7f authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 1.2.13.3

parent b69c70cd

CHANGES.md

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# 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

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@@ -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

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@@ -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

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@@ -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

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@@ -112,9 +112,9 @@ 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.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]