From e6c9c8eb4132db04f3beebb3d9172676d952a8d9 Mon Sep 17 00:00:00 2001
From: Julian Libiseller-Egger <julian.libiseller-egger@nanoporetech.com>
Date: Mon, 2 Oct 2023 18:10:53 +0000
Subject: [PATCH] Update spoa and add `min_coverage` param

---
 CHANGELOG.md | 6 ++++++
 pyspoa.cpp   | 7 ++++---
 setup.py     | 2 +-
 src          | 2 +-
 4 files changed, 12 insertions(+), 5 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 86f120a..2c7523c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,12 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [v0.2.0]
+### Changed
+- Updated SPOA to v4.1.2
+### Added
+- `min_coverage` option recently introduced in SPOA
+
 ## [v0.1.0]
 ### Changed
 - Moved CI to internal infrastructure
diff --git a/pyspoa.cpp b/pyspoa.cpp
index 6b1e27f..c405f47 100644
--- a/pyspoa.cpp
+++ b/pyspoa.cpp
@@ -5,7 +5,7 @@
 using namespace pybind11::literals;  // for _a in pybind def
 
 auto poa(std::vector<std::string> sequences, int algorithm, bool genmsa,
-	 int m, int n, int g, int e, int q, int c) -> pybind11::tuple
+	 int m, int n, int g, int e, int q, int c, int min_coverage) -> pybind11::tuple
 {
     auto alignment_engine = spoa::AlignmentEngine::Create(
       static_cast<spoa::AlignmentType>(algorithm), m, n, g, e, q, c
@@ -18,7 +18,7 @@ auto poa(std::vector<std::string> sequences, int algorithm, bool genmsa,
 	    graph.AddAlignment(alignment, it);
     }
 
-    auto consensus = graph.GenerateConsensus();
+    auto consensus = graph.GenerateConsensus(min_coverage);
     std::vector<std::string> msa;
     if (genmsa)
         msa = graph.GenerateMultipleSequenceAlignment();
@@ -30,7 +30,8 @@ PYBIND11_MODULE(spoa, m) {
     m.def(
        "poa", &poa, "",
        "sequences"_a, "algorithm"_a=0, "genmsa"_a=true,
-       "m"_a=5, "n"_a=-4, "g"_a=-8, "e"_a=-6, "q"_a=-10, "c"_a=-4
+       "m"_a=5, "n"_a=-4, "g"_a=-8, "e"_a=-6, "q"_a=-10, "c"_a=-4,
+       "min_coverage"_a=-1
     );
 
     m.attr("__version__") = VERSION_INFO;
diff --git a/setup.py b/setup.py
index 2df4c65..883b3db 100644
--- a/setup.py
+++ b/setup.py
@@ -139,7 +139,7 @@ def build_extensions(self):
 
 setup(
     name='pyspoa',
-    version='0.1.0',
+    version='0.2.0',
     author='Oxford Nanoporetech Technologies, Ltd.',
     author_email='support@nanoporetech.com',
     url='https://github.com/nanoporetech/pyspoa',
diff --git a/src b/src
index 981ad59..1ab9ab0 160000
--- a/src
+++ b/src
@@ -1 +1 @@
-Subproject commit 981ad5921c989948b37e821f6f47e8e23873cf28
+Subproject commit 1ab9ab076171e5e4f5fcd4d2a2369f26c7f8f48f