Set version to 0.2.8

foerstner-lab · May 9, 2014 · 91d911e · 91d911e
1 parent 549e8a5
commit 91d911e
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Showing 5 changed files with 11 additions and 5 deletions.
diff --git a/CHANGELOG.txt b/CHANGELOG.txt
@@ -1,3 +1,7 @@
+v0.2.8 (2014-05-09)
+- Add removal of crossmapped reads
+- Fix bug in align subcommand (reported by Alexander Mellmann)
+- Adapt description of the DESeq2 installation
 v0.2.7 (2014-05-03)
 - Update docs
 - Improve Makefile

diff --git a/bin/reademption b/bin/reademption
@@ -9,7 +9,7 @@ __author__ = "Konrad Foerstner <[email protected]>"
 __copyright__ = "2011-2014 by Konrad Foerstner <[email protected]>"
 __license__ = "ISC license"
 __email__ = "[email protected]"
-__version__ = "0.2.6"
+__version__ = "0.2.8"
 
 def main():
     parser = argparse.ArgumentParser()

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -50,7 +50,7 @@
 # The short X.Y version.
 version = '0.2'
 # The full version, including alpha/beta/rc tags.
-release = '0.2.7'
+release = '0.2.8'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/reademptionlib/controller.py b/reademptionlib/controller.py
@@ -98,16 +98,18 @@ def align_reads(self):
             self._paths.primary_read_aligner_bam_paths,
             self._paths.unaligned_reads_paths,
             self._paths.primary_read_aligner_stats_path)
+        final_unaligned_reads_paths = self._paths.unaligned_reads_paths
         if self._args.realign is True:
             self._run_realigner_and_process_alignments()
-        if self._args.realign is True:
             self._merge_bam_files()
+            final_unaligned_reads_paths = (
+                self._paths.realigned_unaligned_reads_paths)
         if not self._args.crossalign_cleaning_str is None:
             self._remove_crossaligned_reads()
         self._generate_read_alignment_stats(
             self._lib_names,
             self._paths.read_alignment_bam_paths,
-            self._paths.realigned_unaligned_reads_paths,
+            final_unaligned_reads_paths,
             self._paths.read_alignments_stats_path)
         self._write_alignment_stat_table()
 

diff --git a/setup.py b/setup.py
@@ -5,7 +5,7 @@
 
 setup(
     name='READemption',
-    version='0.2.7',
+    version='0.2.8',
     packages=['reademptionlib', 'tests'],
     author='Konrad U. Förstner',
     author_email='[email protected]',