Updating version number and NEWS

NEWS.md

@@ -4,7 +4,7 @@ stepRNA is available for download at:
 - PyPI: [https://pypi.org/project/stepRNA/](https://pypi.org/project/stepRNA/)
 - Github: [https://github.com/bmm514/stepRNA/releases](https://github.com/bmm514/stepRNA/releases)  
 
-v1.b0 is the first version released to the public, v1.0.3 is the latest version.  
+v1.b0 is the first version released to the public, v1.0.4 is the latest version.  
 
 stepRNA is licensed under the MIT license.  See [LICENSE](./LICENSE) file for details.
 
@@ -17,6 +17,12 @@ Please report any issues to the stepRNA GitHub page or via email:
 
 ## Version Release History
 
+**Version 1.0.4 - 9 Apr, 2021**
+
+- Calcualtion of logodds and Zscores for overlaps
+- Unaligned reads in bowtie alignment removed from BAM output 
+- Full manual still to be added
+
 **Version 1.0.3 - 8 Mar, 2021**
 
 - Updating header in passenger_number.csv to siRNA_sequence

README.md

@@ -35,7 +35,7 @@ In order for stepRNA to run you must have:
 ```pip install stepRNA```
 
 
-**To upgrade to v1.0.3**
+**To upgrade to v1.0.4**
 
 ```pip install --upgrade stepRNA```
 
@@ -44,15 +44,15 @@ If this doesn't work due to non-root access issues see **Installing into a Virtu
 
 **To install from source:**
 
-1) Download [stepRNA-1.0.3.tar.gz](https://pypi.org/project/stepRNA/#files)
+1) Download [stepRNA-1.0.4.tar.gz](https://pypi.org/project/stepRNA/#files)
 2) Unzip it
-3) Move into stepRNA-1.0.3 repository
+3) Move into stepRNA-1.0.4 repository
 4) Run the installation
 
 ```
-tar -xvzf stepRNA-1.0.3.tar.gz
+tar -xvzf stepRNA-1.0.4.tar.gz
 
-cd stepRNA-1.0.3
+cd stepRNA-1.0.4
 
 python3 setup.py install
 ```
@@ -106,9 +106,10 @@ See the [MANUAL](URL_LINK) for more information
 
 Latest release notes:
 
-**Version 1.0.3 - 8 Mar, 2021**
+**Version 1.0.4 - 9 Apr, 2021**
 
-- Updating header in passenger_number.csv to siRNA_sequene
+- Calcualtion of logodds and Zscores for overlaps
+- Unaligned reads in bowtie alignment removed from BAM output 
 - Full manual still to be added
 
 See [NEWS](./NEWS.md) for historical updates of release notes

bin/stepRNA

@@ -58,7 +58,7 @@ optional.add_argument('-d', '--directory', default = os.curdir, help='Directory
 optional.add_argument('-m', '--min_score', default=-1, type=int, help='Minimum score to accept. Default is the shortest read length')
 flags.add_argument('-e', '--remove_exact', action='store_true', help='Remove exact read matches to the reference sequence')
 flags.add_argument('-u', '--make_unique', action='store_true', help='Make FASTA headers unique in reference and reads i.e. >Ref_1 and >Read_1')
-flags.add_argument('-V', '--version', action='version', version='stepRNA v1.0.5', help='Print version number then exit.')
+flags.add_argument('-V', '--version', action='version', version='stepRNA v1.0.4', help='Print version number then exit.')
 
 args = parser.parse_args()
 

setup.py

@@ -4,7 +4,7 @@
     long_description = fh.read()
 
 setuptools.setup(name='stepRNA',
-    version='1.0.3',
+    version='1.0.4',
     author='Ben Murcott',
     author_email='[email protected]',
     description='Align short RNA seqeuncing reads to determine the length of of overhang.',