update version number

CIRI/collapse.py

@@ -295,6 +295,7 @@ def correct_cluster(cluster, is_debug=False, max_cluster=200):
             ss_id, strand, us_shift, ds_shift = ss_site
             circ_start += us_shift
             circ_end += ds_shift
+            circ_type = 'Annotated'
             break
 
     host_strand = find_host_gene(ctg, circ_start, circ_end)

CIRI/version.py

@@ -1 +1 @@
-__version__ = '0.5.0'
+__version__ = '0.6'

README.md

@@ -3,71 +3,22 @@
 [![Build Status](https://travis-ci.com/Kevinzjy/CIRI-long.svg?token=sq9vq2uzixNezTJhts8Z&branch=master)](https://travis-ci.com/Kevinzjy/CIRI-long)
 [![The MIT License](https://img.shields.io/badge/license-MIT-orange.svg)](https://github.com/Kevinzjy/CIRI-long/blob/master/LICENSE)
 
-Circular RNA Identification for Nanopore Sequencing Data
+Circular RNA Identification for Long-Reads Nanopore Sequencing Data
 
-### Author ###
+### Documentation
+
+Documentation is available oneline at https://github.com/Kevinzjy/CIRI-long/wiki
+
+### Author
 
 Authors: Jinyang Zhang([email protected]), Fangqing Zhao([email protected])
 
 Maintainer: Jinyang Zhang
 
-### Release Notes ###
+### Release Notes
 
-- version 0.5.0: reconstruct source code
-- version 0.4.0: add support for fetching circRNAs without full-length structure 
-- version 0.3.0: stringent filter for repeat segments identification
-- version 0.2.0: use minimap / bwapy for bsj detection
-- Version 0.1.0: basic function of CIRI-long
+- version 0.6.0: Update wiki
 
-### License ### 
+### License
 
 The code is released under the MIT License. See the `LICENSE` file for more detail
-
-#### Dependency
-
-- **`gcc 4.8+` or `clang 3.4+` and `cmake 3.2+` is needed**
-- **Only python3 is supported**
-- CIRI-long requires pysam lib, which need executable binary and header of zlib, bzip2, xz, 
-please refer to documentation of [pysam](https://pysam.readthedocs.io/en/latest/installation.html) for installation instructions
-- all python dependencies are listed in `requirements.txt`
-- `samtools` version 1.9 or higher
-- minimap2
-
-#### Installation
-
-You can simply clone the whole repository, then use `make` to start a complete installation 
-
-```bash
-# Clone CIRI-long and submodules
-git clone --recursive https://github.com/Kevinzjy/CIRI-long.git CIRI-long
-cd CIRI-long
-
-# Install CIRI-long 
-make
-
-# Test CIRI-long
-make test
-```
-
-**Note**: for expert users, the installation under virtualenv is highly recommended
-
-```bash
-git clone --recursive https://github.com/Kevinzjy/CIRI-long.git CIRI-long
-cd CIRI-long
-
-# Create virtual environment
-python3 -m venv venv
-
-# Activate virtualenv
-source ./venv/bin/activate
-
-# Install CIRI-long
-make
-
-# Test for installation
-make test
-
-# Deactivate
-deactivate
-```
-