v1.4.2

README.md

@@ -8,15 +8,15 @@
 [![Build Status](https://img.shields.io/travis/yangao07/abPOA/master.svg?label=Master)](https://travis-ci.org/yangao07/abPOA)
 [![License](https://img.shields.io/badge/License-MIT-black.svg)](https://github.com/yangao07/abPOA/blob/master/LICENSE)
 <!-- [![PyPI](https://img.shields.io/pypi/v/pyabpoa.svg?style=flat)](https://pypi.python.org/pypi/pyabpoa) -->
-## Updates (v1.4.1)
+## Updates (v1.4.2)
 
-- Take quality score in FASTQ format file as weight (-Q)
+- Remove cython installation dependency
 
 ## Getting started
 Download the [latest release](https://github.com/yangao07/abPOA/releases):
 ```
-wget https://github.com/yangao07/abPOA/releases/download/v1.4.1/abPOA-v1.4.1.tar.gz
-tar -zxvf abPOA-v1.4.1.tar.gz && cd abPOA-v1.4.1
+wget https://github.com/yangao07/abPOA/releases/download/v1.4.2/abPOA-v1.4.2.tar.gz
+tar -zxvf abPOA-v1.4.2.tar.gz && cd abPOA-v1.4.2
 ```
 Make from source and run with test data:
 ```
@@ -84,9 +84,9 @@ You can also build abPOA from source files.
 Make sure you have gcc (>=6.4.0) and zlib installed before compiling.
 It is recommended to download the [latest release](https://github.com/yangao07/abPOA/releases).
 ```
-wget https://github.com/yangao07/abPOA/releases/download/v1.4.1/abPOA-v1.4.1.tar.gz
-tar -zxvf abPOA-v1.4.1.tar.gz
-cd abPOA-v1.4.1; make
+wget https://github.com/yangao07/abPOA/releases/download/v1.4.2/abPOA-v1.4.2.tar.gz
+tar -zxvf abPOA-v1.4.2.tar.gz
+cd abPOA-v1.4.2; make
 ```
 Or, you can use `git clone` command to download the source code.
 This gives you the latest version of abPOA, which might be still under development.
@@ -98,8 +98,8 @@ cd abPOA; make
 ### <a name="binary"></a>Pre-built binary executable file for Linux/Unix 
 If you meet any compiling issue, please try the pre-built binary file:
 ```
-wget https://github.com/yangao07/abPOA/releases/download/v1.4.1/abPOA-v1.4.1_x64-linux.tar.gz
-tar -zxvf abPOA-v1.4.1_x64-linux.tar.gz
+wget https://github.com/yangao07/abPOA/releases/download/v1.4.2/abPOA-v1.4.2_x64-linux.tar.gz
+tar -zxvf abPOA-v1.4.2_x64-linux.tar.gz
 ```
 
 ## <a name="usage"></a>General usage
@@ -211,7 +211,7 @@ Please refer to the [GFA specification](https://github.com/GFA-spec/GFA-spec/blo
 abPOA can generate a plot of the final partial order alignment graph with the help of `graphviz dot`. 
 For example:
 
-![pog](https://github.com/yangao07/abPOA/blob/master/pog.png)
+![pog](https://github.com/yangao07/abPOA/blob/main/pog.png)
 
 The numbers inside the nodes are the node IDs. The numbers on the edges are the edge weights.
 `S` and `E` are the auxiliary start and end nodes that have no sequence bases.
@@ -249,7 +249,7 @@ With all the similarity scores (minimizer-based Jaccard similarity), abPOA build
 Then, abPOA performs partial order alignment following the order of sequences in this progressive tree set.
 
 ### <a name="mcons"></a>Multiple consensus sequences
-Since v1.4.1, abPOA supports generating multiple consensus sequences from the final alignment graph (set -d/--max-num-cons as >1).
+abPOA supports generating multiple consensus sequences from the final alignment graph (set -d/--max-num-cons as >1).
 
 The general underlying idea is to group input sequences into multiple clusters based on the heterozygous bases in the graph,
 Then, one consensus sequence is separately generated for each cluster of input sequences.

setup.py

@@ -52,7 +52,7 @@
     description = "pyabpoa: SIMD-based partial order alignment using adaptive band",
     long_description = long_description,
     long_description_content_type="text/markdown",
-    version = "1.4.1",
+    version = "1.4.2",
     url = "https://github.com/yangao07/abPOA",
     author = "Yan Gao",
     author_email = "[email protected]",
@@ -65,6 +65,5 @@
                     depends=[src_dir+'abpoa.h', src_dir+'abpoa_align.h', src_dir+'abpoa_graph.h', src_dir+'abpoa_output.h', src_dir+'abpoa_seed.h', src_dir+'abpoa_seq.h', src_dir+'kalloc.h', src_dir+'khash.h', src_dir+'kdq.h', src_dir+'kseq.h', src_dir+'ksort.h', src_dir+'kstring.h', src_dir+'kvec.h', src_dir+'simd_abpoa_align.h', src_dir+'simd_instruction.h', src_dir+'utils.h', 'python/cabpoa.pxd'],
                     libraries = ['z', 'm', 'pthread'],
                     extra_compile_args=['-O3', '-Wno-error=declaration-after-statement', simde, simd_flag])],
-    install_requires=['cython'],
     cmdclass = cmdclass
 )

src/abpoa.c

@@ -16,7 +16,7 @@ char PROG[20] = "abpoa";
 #define _bO BOLD UNDERLINE "O" NONE
 #define _bA BOLD UNDERLINE "A" NONE
 char DESCRIPTION[100] = _ba "daptive " _bb "anded " _bP "artial " _bO "rder " _bA "lignment";
-char VERSION[20] = "1.4.1";
+char VERSION[20] = "1.4.2";
 char CONTACT[30] = "[email protected]";
 
 const struct option abpoa_long_opt [] = {