Merge pull request #51 from ygidtu/dev

v0.0.6

Author: ygidtu

README.md

@@ -137,4 +137,7 @@ contact [Yiming Zhang](https://github.com/ygidtu) and
 
 ## Citation
 
-The citation will be available as soon as possible.
+If you use Sashimi.py in your publication, please cite Sashimi.py by
+
+[Zhang et al. Sashimi.py: a flexible toolkit for combinatorial analysis of genomic data. bioRxiv 2022.11.02.514803.](https://www.biorxiv.org/content/10.1101/2022.11.02.514803v1)
+

docs/index.md

@@ -8,4 +8,4 @@
 
 ## Get started
 
-To learn Snakemake, please follow the [Tutorial](https://sashimi.readthedocs.io/en/latest/command/)
+To learn Sashimi.py, please follow the [Tutorial](https://sashimi.readthedocs.io/en/latest/command/)

sashimi/base/ReadDepth.py

@@ -82,10 +82,19 @@ def __add__(self, other):
                         junctions[i] += j
                     else:
                         junctions[i] = j
+
+            minus = None
+            if self.minus is not None and other.minus is not None:
+                minus = self.minus + other.minus
+            elif self.minus is None and other.minus is not None:
+                minus = other.minus
+            elif self.minus is not None and other.minus is None:
+                minus = self.minus
+
             return ReadDepth(
                 self.plus + other.plus,
                 junctions_dict=junctions,
-                minus=self.minus + other.minus
+                minus=minus
             )
 
     def curr_height(self, pos: int) -> float:

sashimi/cli.py

@@ -21,7 +21,7 @@
 from sashimi.file.ATAC import ATAC
 from sashimi.plot import Plot
 
-__version__ = "0.0.5"
+__version__ = "0.0.6"
 __author__ = "ygidtu & Ran Zhou"
 __email__ = "ygidtu@gmail.com"
 

setup.py

@@ -1,7 +1,7 @@
 import os
 from setuptools import setup, find_packages
 
-__version__ = "0.0.5"
+__version__ = "0.0.6"
 __author__ = "ygidtu & Ran Zhou"
 __email__ = "ygidtu@gmail.com"
 

web/package.json

@@ -1,7 +1,7 @@
 {
   "name": "sashimi.py",
   "private": true,
-  "version": "0.0.5",
+  "version": "0.0.6",
   "type": "module",
   "scripts": {
     "dev": "vite",