write the README and make some cosmetic changes

CMakeLists.txt

@@ -1,6 +1,6 @@
 cmake_minimum_required(VERSION 3.21)
 project(subsetfa
-	VERSION 0.1
+	VERSION 0.5
 	LANGUAGES CXX
 )
 include(CheckCXXCompilerFlag)

README.md

@@ -1 +1,50 @@
-This is a small utility that extracts records from a FASTA file based on names provided in a list file.
+# Overview
+
+This is a small utility that extracts records from a FASTA file based on names provided in a list file. Depends only on a compiler that supports C++-14 and `cmake` version 3.21 or later.
+
+# Download and install
+
+Clone the repository
+
+```sh
+git clone https://github.com/tonymugen/subsetfa
+```
+
+Next, create a build directory
+
+```sh
+cd subsetfa
+mkdir build
+```
+
+Run cmake
+
+```sh
+cd build
+cmake -DCMAKE_BUILD_TYPE=Release ..
+cmake --build .
+cmake --install .
+```
+
+Installation may require root privileges.
+
+# Tests
+
+Optionally, one can also build the unit tests. These require [Catch2](https://github.com/catchorg/Catch2), although its installation is taken care of by `cmake`. To build the tests, create a `build-Tests` directory, say, and run
+
+```sh
+cd build
+cmake -DCMAKE_BUILD_TYPE=Test -DBUILD_TESTS=ON ..
+cmake --build .
+```
+
+To run the tests from the build directory, simply run
+
+```sh
+./tests
+```
+
+# Run the tool
+
+The binary is `subsetfa`. It requires a multi-sequence FASTA file and a list of FASTA headers for sequences to be extracted. Headers must match those in the target FASTA file exactly, those that do not match anything will be ignored. A name of the output FASTA file can also be provided. If not, the default name subset.fasta will be used. The order of records in the output will not necessarily be the same as in the original file. Running `subsetfa` without any arguments will print the command line flag syntax information. 
+

apps/subsetfa.cpp

@@ -21,7 +21,7 @@
 /** \file
  * \author Anthony J. Greenberg
  * \copyright Copyright (c) 2023 Anthony J. Greenberg
- * \version 0.1
+ * \version 0.5
  *
  * Uses the fastaObj methods to extract records from a multi-record FASTA file.
  * Records must be listed in a separate file as FASTA headers that match some in the FASTA file.

include/fastaObj.hpp

@@ -21,7 +21,7 @@
 /** \file
  * \author Anthony J. Greenberg
  * \copyright Copyright (c) 2023 Anthony J. Greenberg
- * \version 0.1
+ * \version 0.5
  *
  * Definitions and interface documentation for the class that holds FASTA file data.
  *

include/utilities.hpp

@@ -21,7 +21,7 @@
 /** \file
  * \author Anthony J. Greenberg
  * \copyright Copyright (c) 2023 Anthony J. Greenberg
- * \version 0.1
+ * \version 0.5
  *
  * Definitions and interface documentation various utility functions.
  *

src/fastaObj.cpp

@@ -21,7 +21,7 @@
 /** \file
  * \author Anthony J. Greenberg
  * \copyright Copyright (c) 2023 Anthony J. Greenberg
- * \version 0.1
+ * \version 0.5
  *
  * Implementation of the class that holds FASTA file data.
  *

src/utilities.cpp

@@ -21,7 +21,7 @@
 /** \file
  * \author Anthony J. Greenberg
  * \copyright Copyright (c) 2023 Anthony J. Greenberg
- * \version 0.1
+ * \version 0.5
  *
  * Implementation of various utility functions.
  *