Merge pull request #16 from hisplan/master

v0.2.9

Author: hisplan

README.md

@@ -38,7 +38,7 @@ To process data locally using SEQC, you must install the <a href=https://github.
 Once all dependencies have been installed, SEQC can be installed by running:
 
 ```bash
-export SEQC_VERSION="0.2.8"
+export SEQC_VERSION="0.2.9"
 wget https://github.com/hisplan/seqc/archive/v${SEQC_VERSION}.tar.gz
 tar xvzf v${SEQC_VERSION}.tar.gz
 cd seqc-${SEQC_VERSION}

docs/README.md

@@ -8,7 +8,7 @@
 
 ## Generating Reference Packages
 
-This generates a reference package (STAR index and GTF) using SEQC v0.2.8.
+This generates a reference package (STAR index and GTF) using SEQC v0.2.9.
 
 - Ensembl 86
 - Gene annotation file that contains only the reference chromosomes (no scaffolds, no patches)

docs/install-SUSE.md

@@ -43,8 +43,8 @@ conda install -c bioconda star
 ## Install SEQC
 
 ```
-wget https://github.com/dpeerlab/seqc/archive/v0.2.8.tar.gz
-tar xvzf v0.2.8.tar.gz
-cd seqc-0.2.8/
+wget https://github.com/dpeerlab/seqc/archive/v0.2.9.tar.gz
+tar xvzf v0.2.9.tar.gz
+cd seqc-0.2.9/
 pip install .
 ```

src/seqc/rmt_correction.py

@@ -414,8 +414,8 @@ def _correct_errors(ra, err_rate, p_value=0.05):
             # skip if it's already marked as rmt error
             if (
                 ra.data["cell"][idx],
-                ra.data["rmt"][idx_corrected_rmt],
                 ra.data["rmt"][idx],
+                ra.data["rmt"][idx_corrected_rmt],
             ) in mapping:
                 continue
 

src/seqc/version.py

@@ -1 +1 @@
-__version__ = "0.2.8"
+__version__ = "0.2.9"