text_align

The purpose of this library is to provide text alignment for large(ish) constant alphabets; in particular alignment of Unicode code points. Currently, it contains a version of the Smith-Waterman algorithm that attempts to split the dynamic programming matrix into blocks and fill them in parallel.

At this point, the library should be considered experimental.

Requirements

• GNU Make

C++ Library

• Compiler that supports C++17, e.g. GCC 8 or Clang 7
• Boost (tested with version 1.68)
• To build the provided command line tool, GNU Gengetopt is also required.
• The supporting library, libbio, requires Ragel at compile time.

Python Extension

• Python 3 (tested with version 3.6)
• setuptools
• Cython

PostgreSQL Extension

• Tested with version 10.4

Building

Running make in the project root builds the C++ library, the command line tool and the unit tests. Running make clean cleans everything including the PostgreSQL and Python extensions.

1. Edit local.mk. Useful variables include CC, CXX, PYTHON, EXTRA_CFLAGS, EXTRA_CXXFLAGS and EXTRA_LDFLAGS.
2. Run make.
3. To build either of the extensions, change to the subdirectory in question and run make.