CHANGES.md

 # 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>`_. 

debian/changelog

+paleomix (1.2.13.3-1) unstable; urgency=medium
+
+  * New upstream version
+  * Standards-Version: 4.2.1
+  * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
+  * Do not use tox to run full test suite in autopkgtest since it relies
+    on full source dir
+
+ -- Andreas Tille <tille@debian.org>  Mon, 17 Dec 2018 13:35:27 +0100
+
 paleomix (1.2.13.2-1) unstable; urgency=medium
 
   * Should be architecture any since it build-depends on the amd64-only

debian/control

@@ -15,7 +15,7 @@ Build-Depends: debhelper (>= 11~),
                default-jre-headless,
                bowtie2,
                rsync
-Standards-Version: 4.1.4
+Standards-Version: 4.2.1
 Vcs-Browser: https://salsa.debian.org/med-team/paleomix
 Vcs-Git: https://salsa.debian.org/med-team/paleomix.git
 Homepage: http://geogenetics.ku.dk/publications/paleomix

debian/rules

@@ -11,11 +11,13 @@ export PYBUILD_TEST_ARGS = --exclude='(test_requirementobj__version__command_not
 	dh $@ --with python2 --buildsystem=pybuild
 
 override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	# apply fix that seems to be needed due to improperly set
 	# time zone in pbuilder
 	sed -i~ 's/"MTime": "2005-07-07 08:50:00"/"MTime": "2005-07-07 06:50:00"/' tests/common_tests/makefile_test.py
 	PATH=$(CURDIR)/bin/:$(PATH) dh_auto_test
 	mv tests/common_tests/makefile_test.py~ tests/common_tests/makefile_test.py
+endif
 
 override_dh_install:
 	dh_install
@@ -43,3 +45,7 @@ override_dh_installdocs:
 	#find debian -name "empty_file*"
 	#find debian -name "timestamp_*"
 	#echo "======  Hope something was printed between these lines ===="
+	#
+	# This test tries to execute setup.sh which does not work outside source directory
+	find debian/$(DEB_SOURCE)/usr/share/doc/ -name fileutils_test.py -delete
+	find debian/$(DEB_SOURCE)/usr/share/doc/ -name setup.h -delete

debian/tests/control

 Tests: run-unit-test
-Depends: @, tox
+Depends: @
 Restrictions: allow-stderr

debian/tests/run-unit-test

@@ -19,4 +19,7 @@ for gz in `find . -name "*.gz"` ; do
     fi
 done
 
-tox
\ No newline at end of file
+## tox needs to run in source dir and relies on files only available in full source
+# tox
+## so rather run some test that is part of the tox test suite
+nosetests --with-coverage --cover-erase --cover-inclusive --cover-tests --cover-package paleomix .
\ No newline at end of file

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

@@ -112,9 +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]