From 138407dcf01d0a147a5b98931a96c6cfe6694775 Mon Sep 17 00:00:00 2001
From: Yan Gao <yangao@ds.dfci.harvard.edu>
Date: Wed, 18 Sep 2024 15:23:26 -0400
Subject: [PATCH] v1.5.3

---
 README.md   | 26 +++++++++++++-------------
 TODO.md     |  9 ---------
 setup.py    |  2 +-
 src/abpoa.c |  2 +-
 4 files changed, 15 insertions(+), 24 deletions(-)
 delete mode 100644 TODO.md

diff --git a/README.md b/README.md
index 7131b63..9bdb13e 100644
--- a/README.md
+++ b/README.md
@@ -8,16 +8,16 @@
 [![C/C++ CI](https://github.com/yangao07/abPOA/actions/workflows/linux-CI.yml/badge.svg)](https://github.com/yangao07/abPOA/actions/workflows/linux-CI.yml)
 [![C/C++ CI](https://github.com/yangao07/abPOA/actions/workflows/macos-CI.yml/badge.svg)](https://github.com/yangao07/abPOA/actions/workflows/macos-CI.yml)
 [![License](https://img.shields.io/badge/License-MIT-black.svg)](https://github.com/yangao07/abPOA/blob/main/LICENSE)
-## Updates (v1.5.2)
+## Updates (v1.5.3)
 
-- Fix a backtrack bug in seeding mode
-- Add consensus mode: most frequent base at each pos
+- Fix a score matrix bug in pyabpoa
+- Add consensus mode for pyabpoa: most frequent base at each pos
 
 ## Getting started
 Download the [latest release](https://github.com/yangao07/abPOA/releases):
 ```
-wget https://github.com/yangao07/abPOA/releases/download/v1.5.2/abPOA-v1.5.2.tar.gz
-tar -zxvf abPOA-v1.5.2.tar.gz && cd abPOA-v1.5.2
+wget https://github.com/yangao07/abPOA/releases/download/v1.5.3/abPOA-v1.5.3.tar.gz
+tar -zxvf abPOA-v1.5.3.tar.gz && cd abPOA-v1.5.3
 ```
 Make from source and run with test data:
 ```
@@ -35,7 +35,7 @@ abpoa ./test_data/seq.fa > cons.fa
 ## Table of Contents
 
 - [abPOA: adaptive banded Partial Order Alignment](#abpoa-adaptive-banded-partial-order-alignment)
-  - [Updates (v1.5.2)](#updates-v152)
+  - [Updates (v1.5.3)](#updates-v152)
   - [Getting started](#getting-started)
   - [Table of Contents](#table-of-contents)
   - [Introduction](#introduction)
@@ -94,9 +94,9 @@ 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/v1.5.2/abPOA-v1.5.2.tar.gz
-tar -zxvf abPOA-v1.5.2.tar.gz
-cd abPOA-v1.5.2; make
+wget https://github.com/yangao07/abPOA/releases/download/v1.5.3/abPOA-v1.5.3.tar.gz
+tar -zxvf abPOA-v1.5.3.tar.gz
+cd abPOA-v1.5.3; 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.
@@ -108,13 +108,13 @@ cd abPOA; make
 ### Pre-built binary executable file for Linux/Unix or MacOS
 If you meet any compiling issue, please try the pre-built binary file for linux:
 ```
-wget https://github.com/yangao07/abPOA/releases/download/v1.5.2/abPOA-v1.5.2_x64-linux.tar.gz
-tar -zxvf abPOA-v1.5.2_x64-linux.tar.gz
+wget https://github.com/yangao07/abPOA/releases/download/v1.5.3/abPOA-v1.5.3_x64-linux.tar.gz
+tar -zxvf abPOA-v1.5.3_x64-linux.tar.gz
 ```
 or for macos:
 ```
-wget https://github.com/yangao07/abPOA/releases/download/v1.5.2/abPOA-v1.5.2_arm64-macos.tar.gz
-tar -zxvf abPOA-v1.5.2_arm64-macos.tar.gz
+wget https://github.com/yangao07/abPOA/releases/download/v1.5.3/abPOA-v1.5.3_arm64-macos.tar.gz
+tar -zxvf abPOA-v1.5.3_arm64-macos.tar.gz
 ```
 
 ## General usage
diff --git a/TODO.md b/TODO.md
deleted file mode 100644
index 3c7e96d..0000000
--- a/TODO.md
+++ /dev/null
@@ -1,9 +0,0 @@
-# To test after commit
-1. run through
-   1. SSE/AVX2/AVX512
-   2. 16/32bits
-   3. global/local
-   4. lg/ag/cg
-2. same result
-   1. SSE vs AVX2 vs AVX512
-   2. 16bits vs 32 bits
\ No newline at end of file
diff --git a/setup.py b/setup.py
index f2f0608..40cbec6 100644
--- a/setup.py
+++ b/setup.py
@@ -63,7 +63,7 @@
     description = "pyabpoa: SIMD-based partial order alignment using adaptive band",
     long_description = long_description,
     long_description_content_type="text/markdown",
-    version = "1.5.2",
+    version = "1.5.3",
     url = "https://github.com/yangao07/abPOA",
     author = "Yan Gao",
     author_email = "yangao@ds.dfci.harvard.edu",
diff --git a/src/abpoa.c b/src/abpoa.c
index a18895f..0ee6df7 100644
--- a/src/abpoa.c
+++ b/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] = "1.5.2";
+char VERSION[20] = "1.5.3";
 char CONTACT[30] = "yangao@ds.dfci.harvard.edu";
 
 const struct option abpoa_long_opt [] = {