samtools-ruby

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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