Update minimap2 to v2.27 and use faster HQ ONT alignment

flye/polishing/alignment.py

@@ -241,7 +241,7 @@ def _run_minimap(reference_file, reads_files, num_proc, reads_type, out_file):
     elif reads_type in ["nano-raw", "nano-corrected"]:
         mode = "map-ont"
     elif reads_type == "nano-nano_hq":
-        mode = "map-ont"
+        mode = "lr:hq"
         extra_args = ["-k", "17"]
 
     cmdline = [MINIMAP_BIN, "'" + reference_file + "'"]

lib/minimap2/.github/workflows/ci.yaml

@@ -0,0 +1,21 @@
+name: CI
+
+on:
+  push:
+    branches:
+    - master
+  pull_request:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        compiler: [gcc, clang]
+
+    steps:
+    - name: Checkout minimap2
+      uses: actions/checkout@v2
+
+    - name: Compile with ${{ matrix.compiler }}
+      run:  make CC=${{ matrix.compiler }}

lib/minimap2/.gitignore

@@ -0,0 +1,8 @@
+.cproject
+.project
+.*.swp
+*.a
+*.o
+*.dSYM
+minimap2
+mappy.c

lib/minimap2/.gitmodules

@@ -0,0 +1,3 @@
+[submodule "lib/simde"]
+	path = lib/simde
+	url = https://github.com/nemequ/simde.git

lib/minimap2/LICENSE 2.txt

@@ -0,0 +1,24 @@
+The MIT License
+
+Copyright (c) 2018-     Dana-Farber Cancer Institute
+              2017-2018 Broad Institute, Inc.
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

lib/minimap2/Makefile

@@ -30,12 +30,12 @@ endif
 
 ifneq ($(asan),)
 	CFLAGS+=-fsanitize=address
-	LIBS+=-fsanitize=address
+	LIBS+=-fsanitize=address -ldl
 endif
 
 ifneq ($(tsan),)
 	CFLAGS+=-fsanitize=thread
-	LIBS+=-fsanitize=thread
+	LIBS+=-fsanitize=thread -ldl
 endif
 
 .PHONY:all extra clean depend