Use ksw2 to align soft-clipped ends from ungapped alignment

CHANGES.md

@@ -21,6 +21,9 @@
 * Include [ZStr](https://github.com/mateidavid/zstr/) in our own repository
   instead of downloading it at build time. This should make it possible to
   build strobealign without internet access.
+* #357: Fix some suboptimal alignment ends. Sometimes an end was soft-clipped
+  although a better alignment with an insertion or deletion existed that
+  extends to the end of the read.
 
 ## v0.12.0 (2023-11-23)
 

CMakeLists.txt

@@ -63,6 +63,7 @@ add_library(salib STATIC ${SOURCES}
   ext/xxhash.c
   ext/ssw/ssw_cpp.cpp
   ext/ssw/ssw.c
+  ext/ksw2/ksw2_extz2_sse.c
 )
 target_include_directories(salib PUBLIC src/ ext/ ${PROJECT_BINARY_DIR})
 target_link_libraries(salib PUBLIC ZLIB::ZLIB Threads::Threads zstr::zstr)

ext/README.md

@@ -60,3 +60,10 @@ License: See xxhash.c
 Homepage: https://github.com/mateidavid/zstr
 Commit used: 755da7890ea22478a702e3139092e6c964fab1f5
 License: See zstr/LICENSE
+
+
+## ksw2
+
+https://github.com/lh3/ksw2
+https://raw.githubusercontent.com/lh3/ksw2/06b2183b0f6646d82f2e3f5884008a1b4582f5b5/ksw2.h
+https://raw.githubusercontent.com/lh3/ksw2/06b2183b0f6646d82f2e3f5884008a1b4582f5b5/ksw2_extz2_sse.c

ext/ksw2/LICENSE.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.