Merge pull request #13 from hisplan/master

v0.2.8

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="0.2.6"
+export SEQC_VERSION="0.2.8"
 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 v0.2.6.
+This generates a reference package (STAR index and GTF) using SEQC v0.2.8.
 
 - 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/v0.2.6.tar.gz
-tar xvzf v0.2.6.tar.gz
-cd seqc-0.2.6/
+wget https://github.com/dpeerlab/seqc/archive/v0.2.8.tar.gz
+tar xvzf v0.2.8.tar.gz
+cd seqc-0.2.8/
 pip install .
 ```

src/seqc/core/run.py

@@ -283,6 +283,10 @@ def create_read_array(
         ):
             args.filter_low_coverage = False
 
+        if args.platform == "ten_x_v2" or args.platform == "ten_x_v3":
+            log.notify("Setting min_poly_t=0 for 10x v2 & v3")
+            args.min_poly_t = 0            
+
         max_insert_size = args.max_insert_size
         if args.filter_mode == "scRNA-seq":
             # for scRNA-seq

src/seqc/version.py

@@ -1 +1 @@
-__version__ = "0.2.7"
+__version__ = "0.2.8"