From 53a7c0a2b9159343ed65de3097a095cde35a5abf Mon Sep 17 00:00:00 2001
From: Benedetto Polimeni <bpolimeni@gmail.com>
Date: Wed, 17 Jul 2024 10:26:48 +0000
Subject: [PATCH 1/4] remove commented code

---
 irescue/main.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/irescue/main.py b/irescue/main.py
index 13f1089..736812f 100644
--- a/irescue/main.py
+++ b/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 "

From 40acb4a2c1093114625b1d36d737981d4f607b7f Mon Sep 17 00:00:00 2001
From: Benedetto Polimeni <bpolimeni@gmail.com>
Date: Wed, 17 Jul 2024 13:23:16 +0000
Subject: [PATCH 2/4] ignore conda env with ".conda" prefix

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index e45759d..2cb1ec6 100644
--- a/.gitignore
+++ b/.gitignore
@@ -109,6 +109,7 @@ venv/
 ENV/
 env.bak/
 venv.bak/
+.conda
 
 # Spyder project settings
 .spyderproject

From 6cb9c9ad47f8212673c11003f983cef645cace15 Mon Sep 17 00:00:00 2001
From: Benedetto Polimeni <bpolimeni@gmail.com>
Date: Fri, 23 Aug 2024 15:54:21 +0000
Subject: [PATCH 3/4] bump 1.1.0

---
 irescue/_version.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/irescue/_version.py b/irescue/_version.py
index 236fd8c..1a72d32 100644
--- a/irescue/_version.py
+++ b/irescue/_version.py
@@ -1 +1 @@
-__version__ = '1.1.0-beta.2'
+__version__ = '1.1.0'

From 09d0e89f71155de83ac4d7c60febc951e506b522 Mon Sep 17 00:00:00 2001
From: Benedetto Polimeni <bpolimeni@gmail.com>
Date: Fri, 23 Aug 2024 15:58:44 +0000
Subject: [PATCH 4/4] Update description

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 49519cf..7a8b188 100644
--- a/README.md
+++ b/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