Update README.md

README.md

@@ -1,40 +1,49 @@
 readpaf
 =======
-Scripts for reading minimap2 PAF files
+[![Build](https://github.com/alexomics/read-paf/actions/workflows/main.yml/badge.svg)](https://github.com/alexomics/read-paf/actions/workflows/main.yml)
+[![PyPI](https://img.shields.io/pypi/v/readpaf)](https://pypi.org/p/readpaf)
 
-Installation
-===
+readpaf is a fast parser for [minimap2](https://github.com/lh3/minimap2) PAF (**P**airwise m**A**pping **F**ormat) files. It is 
+pure python with no dependencies (unless you want a DataFrame).
 
-readpaf is contained in a single module so can be installed via PyPI:
 
+Installation
+===
 ```bash
 pip install readpaf
 ```
 
-inlcuding pandas:
-
-```bash
-pip install readpaf[pandas]
-```
-
-Or [readpaf.py](readpaf.py) can be directly downloaded like so
+<details>
+  <summary>Other install methods</summary>
+
+   ### Install with pandas:
+   This is only needed if you want to manipulate the PAF file as a `pandas.DataFrame`
 
-using cURL
+   ```bash
+   pip install readpaf[pandas]
+   ```
 
-```bash
-curl -O https://raw.githubusercontent.com/alexomics/read-paf/main/readpaf.py
-```
+   ### Direct download:
+   using cURL
 
-or wget
+   ```bash
+   curl -O https://raw.githubusercontent.com/alexomics/read-paf/main/readpaf.py
+   ```
 
-```bash
-wget https://raw.githubusercontent.com/alexomics/read-paf/main/readpaf.py
+   or wget
 
-```
+   ```bash
+   wget https://raw.githubusercontent.com/alexomics/read-paf/main/readpaf.py
+   ```
+</details>
 
 Usage
 ===
 
+readpaf only has one user function, `parse_paf` that accepts of file-like object; this 
+is any object in python that has a file-oriented API (`sys.stdin`, `stdout` from subprocess, 
+`io.StringIO`, open files from `gzip` or `open`).  
+
 The following script demonstrates how minimap2 output can be piped into read-paf 
 
 ```python
@@ -43,7 +52,6 @@ from sys import stdin
 
 for record in parse_paf(stdin):
     print(record.query_name, record.target_name)
-
 ```
 
 read-paf can also generate a pandas DataFrame:
@@ -81,7 +89,10 @@ Parameters:
 
 If used as an iterator, then each object returned is a named tuple representing a single line in the PAF file. 
 Each named tuple has field names as specified by the `fields` parameter. The SAM-like tags are converted into 
-their correct types and stored in a dictionary.
+their correct types and stored in a dictionary. When `print` or `str` are called on `PAF` record (named tuple) 
+a formated PAF string is returned, which is useful for writing records to a file. The `PAF` record also has a 
+method `blast_identity` which calculates the [blast identity](https://lh3.github.io/2018/11/25/on-the-definition-of-sequence-identity) for
+that record.
 
 If used to generate a pandas DataFrame, then each row represents a line in the PAF file and the SAM-like tags 
 are expanded into individual series.