README

samtools-ruby

Intrduction
Binder of samtools for ruby, on the top of FFI. 

This project was born from the need to add support of BAM files to 
the gee_fu genome browser (http://github.com/danmaclean/gee_fu). 

Installation
At the moment, the only way to "install" the module is to copy it to copy the content 
of the lib folder on any lib folder you have. You must also copy your libbam.a (linux)
or libbam.dll (windows) from samtools. If you have a Mac, add the following variable
to the makefile of samtools

DYFLAGS 	= -dynamiclib -lz

and the following target:
dylib: libbam.dylib
libbam.dylib:$(LOBJS)
		$(CC) $(CFLAGS) $(DYFLAGS) -o libbam.dylib $(LOBJS)

Then, run 

make dylib

Finally, you copy the .dylib file to your lib folder. 

Usage
The easiest way to see in "action" samtools-ruby to call
rake test. 


Dependencies:
-FFI (http://github.com/ffi/ffi)
-libbam
	This can be obtained from samtools.  (http://samtools.sourceforge.net/ )

LICENSE
This wrapper is available under GPLv3. 
	
FAQ.
I´m getting a segmentation Fault, what did I do wrong?
There are two known segmentation faults at the moment
	-When you try to load a text file as binary file
	-When you try to lad a binary file as a text file

If this is not the problem, or you have any other question,  don´t hesitate on 
dropping a line to
Ricardo dot Ramirez-Gonzalez at bbsrc dot ac dot uk

TODO
-Write a gem to install it
-Filter to the fetching algorithm (give a condition that has to be satisfied to add the alignment to the list)
-Examples of how to use it, besides the test folder