Merge branch 'release/1.6.0'

.licenserc.yaml

@@ -3,7 +3,7 @@ header:
     spdx-id: AGPL-3.0-or-later
     copyright-owner: Genome Research Ltd
     content: |
-      Copyright (c) 2021
+      Copyright (c) 2021-2022
 
       Author: CASM/Cancer IT <[email protected]>
 
@@ -33,7 +33,7 @@ header:
       2009, 2010, 2011, 2012’.
 
     pattern: |
-      Copyright \(c\) \d+
+      Copyright \(c\) \d+.*
 
       Author: .+
 
@@ -80,5 +80,6 @@ header:
     - 'MANIFEST.in'
     - 'tests/htmlcov/'
     - '.eggs/'
+    - 'publication/'
 
   comment: on-failure

CHANGES.md

@@ -1,5 +1,9 @@
 # CHANGES
 
+## 1.6.0
+
+Adds example data used in publication.
+
 ## 1.5.1
 
 - Improve outputs when `R2_R1` has been applied to ensure input fields are replicated "as is" in counts file

README.md

@@ -1,42 +1,43 @@
 # pyCROQUET
 
-python Crispr Read to Oligo QUantification Enhancement Tool
+python Crispr Read to Oligo QUantification and Evaluation Tool
 
 [![cancerit](https://circleci.com/gh/cancerit/pycroquet.svg?style=svg)](https://circleci.com/gh/cancerit/pycroquet)
 
-- [Publications](#publications)
-- [General](#general)
-- [Subcommands](#subcommands)
-- [Options](#options)
-  - [`guidelib`](#guidelib)
-  - [`queries`](#queries)
-  - [`chunks`](#chunks)
-  - [`rules`](#rules)
-- [Output files](#output-files)
-  - [CRAM](#cram)
-    - [Reads mapping to a `sgrna_id`](#reads-mapping-to-a-sgrna_id)
-    - [Reads assigned to a guide](#reads-assigned-to-a-guide)
-- [Dual guide](#dual-guide)
-  - [Statistic file extension](#statistic-file-extension)
-- [Boundary mode details](#boundary-mode-details)
-  - [`exact`](#exact)
-  - [`TinQ` - target in query](#tinq---target-in-query)
-  - [`QinT` - query in target](#qint---query-in-target)
-  - [`any`](#any)
-- [Viewing alignments](#viewing-alignments)
-- [Installation](#installation)
-  - [Pypi](#pypi)
-  - [Docker and Singularity](#docker-and-singularity)
-- [Development](#development)
-  - [Linux](#linux)
-  - [Mac](#mac)
-- [Testing](#testing)
-  - [Local `venv` testing](#local-venv-testing)
-  - [Local `pre-commit` hooks](#local-pre-commit-hooks)
-  - [Docker testing](#docker-testing)
-  - [CI tests](#ci-tests)
-  - [Updating licence headers](#updating-licence-headers)
-- [LICENSE](#license)
+- [pyCROQUET](#pycroquet)
+  - [Publications](#publications)
+  - [General](#general)
+  - [Subcommands](#subcommands)
+  - [Options](#options)
+    - [`guidelib`](#guidelib)
+    - [`queries`](#queries)
+    - [`chunks`](#chunks)
+    - [`rules`](#rules)
+  - [Output files](#output-files)
+    - [CRAM](#cram)
+      - [Reads mapping to a `sgrna_id`](#reads-mapping-to-a-sgrna_id)
+      - [Reads assigned to a guide](#reads-assigned-to-a-guide)
+  - [Dual guide](#dual-guide)
+    - [Statistic file extension](#statistic-file-extension)
+  - [Boundary mode details](#boundary-mode-details)
+      - [`exact`](#exact)
+      - [`TinQ` - target in query](#tinq---target-in-query)
+      - [`QinT` - query in target](#qint---query-in-target)
+      - [`any`](#any)
+  - [Viewing alignments](#viewing-alignments)
+  - [Installation](#installation)
+    - [Pypi](#pypi)
+    - [Docker and Singularity](#docker-and-singularity)
+  - [Development](#development)
+    - [Linux](#linux)
+    - [Mac](#mac)
+  - [Testing](#testing)
+    - [Local `venv` testing](#local-venv-testing)
+    - [Local `pre-commit` hooks](#local-pre-commit-hooks)
+    - [Docker testing](#docker-testing)
+    - [CI tests](#ci-tests)
+    - [Updating licence headers](#updating-licence-headers)
+  - [LICENSE](#license)
 
 ## Publications
 
@@ -397,7 +398,7 @@ If you need to make more extensive changes to the license carefully test the pat
 ## LICENSE
 
 ```
-Copyright (c) 2021
+Copyright (c) 2021-2022
 
 Author: CASM/Cancer IT <[email protected]>