bio-samtools

The original project samtools-ruby belongs to Ricardo H. Ramirez @ github.com/homonecloco/samtools-ruby

Introduction

Documentation and code come from that project and we’ll adapt it for a better integration in BioRuby.

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

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 -Operating system independent, DONE ( test needed)

IMPORTANT NOTE

-Libraries are compiled for 64 bit machines -The gem/archive comes with preinstalled library .a and dylib, .dll is missing I didn’t compile it. -Library .a, I didn’t check if it works on linux (test needed) -Library libbam.so.1, The library is simply compiled with make dylib without any special parameter on CentOS5.5 x86_64, gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-48). $ openssl dgst libbam.so.1 MD5(libbam.so.1)= c45cfccfb41ffeb2730ee4b227d244c4

Contributing to bio-samtools

Check out the latest master to make sure the feature hasn’t been implemented or the bug hasn’t been fixed yet
Check out the issue tracker to make sure someone already hasn’t requested it and/or contributed it
Fork the project
Start a feature/bugfix branch
Commit and push until you are happy with your contribution
Make sure to add tests for it. This is important so I don’t break it in a future version unintentionally.
Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.