[med-svn] [Git][med-team/paleomix][upstream] New upstream version 1.2.13.3

[Andreas Tille]

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

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