'''
Created on Oct 25, 2012

@author: <NAME>
'''

from distutils.core import setup
import lapels.version

setup(
    name = 'lapels',
    version = lapels.version.__version__,
    description = 'Lapels - A remapper and annotator of in silico (pseudo) genome alignments',
    author = '<NAME>',
    author_email = '<EMAIL>',
    url='http://code.google.com/p/lapels/',    
    license='The MIT License',    
    platforms=['Linux',],    
    packages = ['lapels', 'modtools'],
    scripts = ['lapels/scripts/pylapels', 'lapels/scripts/fixmate',
               'modtools/scripts/vcf2mod','modtools/scripts/insilico',
               'modtools/scripts/modstat'],
    install_requires = ['pysam>=0.6b', 'argparse>=1.2'],
    dependency_links = ['http://lapels.googlecode.com/files/pysam-0.6b.tar.gz',],    
    keywords = 'lapels remap position bam mod',
    long_description='''
Lapels remaps reads aligned to the in silico genome back to the reference 
coordinate and annotates variants.

Two files are taken as input:
    (1) a MOD file that is used to generate the in silico genome and
    (2) a BAM file that contains the in silico genome alignments.
    
Lapels will generate a new BAM file with corrected read positions, adjusted 
cigar strings, and annotated tags of variants (eg. SNPs, Insertions, and 
Deletions).      
''',
)