SRMA - short read micro re-aligner 

There are two version of SRMA currently:
1. A C-version found in the c-code sub-directory.
2. A Java version found in the java sub-directory.

=== To Install ===

==== Java ====
1. Move into the java sub-directory.

2. Download sam-1.39.jar and picard-1.39.jar and place them in a folder 
called lib.

3. Run:
 ant jar

==== C-code ====
1. Move into the c-code sub-directory.

2. Run:
 sh autogen.sh && ./configure && make

See the README in the sub-directory for more help.

=== For more help ===

see http://srma.sf.net