Merge pull request #17 from bodegalab/dev

Minor adjustments to docs and syntax

.gitignore

@@ -109,6 +109,7 @@ venv/
 ENV/
 env.bak/
 venv.bak/
+.conda
 
 # Spyder project settings
 .spyderproject

README.md

@@ -8,7 +8,7 @@
 # IRescue - <ins>I</ins>nterspersed <ins>Re</ins>peats <ins>s</ins>ingle-<ins>c</ins>ell q<ins>u</ins>antifi<ins>e</ins>r
 
 <img align="right" height="160" src="docs/logo.png">
-IRescue quantifies the expression fo transposable elements (TEs) subfamilies in single cell RNA sequencing (scRNA-seq) data that performs UMI-deduplication with sequencing errors correction considering all TE subfamilies associated to multi-mapping reads. TE counts are written on a sparse matrix (similar to Cell Ranger's output) compatible with Seurat, Scanpy and other toolkits.
+IRescue quantifies the expression fo transposable elements (TEs) subfamilies in single cell RNA sequencing (scRNA-seq) data, performing UMI-deduplication with sequencing errors correction and probabilistic assignment of multi-mapping reads by Expectation-Maximization (EM). The output is written on a sparse matrix compatible with Seurat, Scanpy and other toolkits.
 
 ## Content
 

irescue/_version.py

@@ -1 +1 @@
-__version__ = '1.1.0-beta.2'
+__version__ = '1.1.0'

irescue/main.py

@@ -72,9 +72,6 @@ def parseArguments():
                         "presence in bam file.")
     parser.add_argument('--keeptmp', action='store_true',
                         help="Keep temporary files under <output_dir>/tmp.")
-    #parser.add_argument('--tmpdir', default='irescue_out/tmp', metavar='DIR',
-    #                    help="Directory to store temporary files "
-    #                    "(default: %(default)s).")
     parser.add_argument('-v', '--verbose', action='store_true',
                         help="Writes a lot of stuff to stderr, such as "
                         "chromosomes as they are mapped and cell barcodes "