From 7e70afd5070329da019fa8306867b430242de05a Mon Sep 17 00:00:00 2001
From: Kiarod Pashminehazar <142354008+kiarod@users.noreply.github.com>
Date: Wed, 28 Aug 2024 09:20:41 -0700
Subject: [PATCH] Kpash update pysam version (#101)

* bump pipeval version to 0.22.1

* fix typo

* update CHANGELOG
---
 CHANGELOG.md |  3 ++-
 README.md    | 40 ++++++++++++++++++++++++----------------
 setup.cfg    |  4 ++--
 3 files changed, 28 insertions(+), 19 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9475126..f0f51a9 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,7 +8,8 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 ---
 
 ## [Unreleased]
-
+### Changed
+- Update `pysam` version to `0.22.1`
 ---
 
 ## [5.1.0] - 2024-07-08
diff --git a/README.md b/README.md
index b6cabc5..4b1e70c 100644
--- a/README.md
+++ b/README.md
@@ -1,21 +1,29 @@
 # PipeVal
 
-- [Overview](#overview)
+- [PipeVal](#pipeval)
+  - [Overview](#overview)
     - [Validation Flowchart](#validation-flowchart)
-- [Docker](#docker)
-- [Installation](#installation)
-    - [From GitHub](#install-directly-from-github)
-    - [From local](#install-from-cloned-repository)
-- [Usage](#usage)
-    - [validate](#validate)
-        - [Supported Types](#supported-types)
-        - [Expected Output](#expected-output)
-    - [generate-checksum](#generate-checksum)
-- [Development](#development)
-- [References](#references)
-- [Discussions](#discussions)
-- [Contributors](#contributors)
-- [License](#license)
+  - [Docker](#docker)
+  - [Installation](#installation)
+    - [Installing `libmagic`](#installing-libmagic)
+    - [Install directly from GitHub through SSH](#install-directly-from-github-through-ssh)
+    - [Install directly from GitHub through HTTPS](#install-directly-from-github-through-https)
+    - [Install from cloned repository](#install-from-cloned-repository)
+  - [Usage](#usage)
+    - [`pipeval validate`](#pipeval-validate)
+      - [Supported Types](#supported-types)
+      - [Expected Output](#expected-output)
+      - [Validation Skipping](#validation-skipping)
+    - [`pipeval generate-checksum`](#pipeval-generate-checksum)
+  - [Development](#development)
+  - [References](#references)
+    - [Pysam](#pysam)
+      - [Publications](#publications)
+    - [VCFtools](#vcftools)
+      - [Publications](#publications-1)
+  - [Discussions](#discussions)
+  - [Contributors](#contributors)
+  - [License](#license)
 
 ## Overview
 PipeVal is an easy to use CLI tool that can be used to validate different inputs and parameters in various settings, including Nextflow scripts/pipelines. It can be used standalone or using a Docker container.
@@ -91,7 +99,7 @@ options:
   -t, --test-integrity  Whether to perform a full integrity test on compressed files
 ```
 
-The tool will attempt to automatically detect the file type based on extension and perform the approriate validations. The tool will also perform an existence check along with a checksum check if an MD5 or SHA512 checksum exists regardless of file type.
+The tool will attempt to automatically detect the file type based on extension and perform the appropriate validations. The tool will also perform an existence check along with a checksum check if an MD5 or SHA512 checksum exists regardless of file type.
 
 #### Supported Types
 
diff --git a/setup.cfg b/setup.cfg
index aa7cb7b..75ab984 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -15,7 +15,7 @@ classifiers =
     Operating System :: OS Independent
 
 [options]
-package_dir = 
+package_dir =
     = .
 packages = find:
 python_requires = >=3.6
@@ -23,7 +23,7 @@ python_requires = >=3.6
 install_requires =
     mock==4.0.2
     pytest==7.2.2
-    pysam==0.19.0
+    pysam==0.22.1
     python-magic==0.4.27
 
 [options.packages.find]