djhshih / mlat

Minimal BLAT

MLAT: Minimal BLAT

MLAT is a tool for sequence alignment.

This is a fork of the BLAT package (v35) written by Jim Kent. The package has been significantly restructured and stripped down to minimize code footprint. Header and source files have been modified, and minimal C and C++ API's are now provided.

This package itself is licensed under GPLv3. Use of BLAT (and hence MLAT) is subject to the terms of the BLAT non-commercial license (see LICENSE_blat.txt).

Installation

Required: gcc >= 5.2, make

You can simply

make install

Thereupon, binaries, libraries, and headers will be installed in build/. To install to some other location (e.g. /usr/local),

make install DESTDIR=/usr/local

Known bugs

Code compilation was tested with

gcc-4.4.7
gcc-5.2.0
gcc-5.4.0
gcc-6.3.0
clang-3.5

The code is not compatible with -O2 and -O3 optimization flags when compiled with gcc-4.4.7. Use -O2 or -O3 only when compiling with gcc-5.2.0 or higher.

Unit tests were built using programs compiled with clang-3.5. Moderate differences exist when compiled using a different compiler. Sometimes, programs also produce moderate differences for different compilations with the same compiler: the cause of these differences is inherited upstream from BLAT and remains unresolved.