Metadata-Version: 1.1
Name: cigar
Version: 0.1.3
Summary: manipulate SAM cigar strings
Home-page: https://github.com/brentp/cigar
Author: Brent Pedersen
Author-email: bpederse@gmail.com
License: MIT
Description: Cigar
        =====
        
        cigar is a simple library for dealing with cigar strings. the most useful
        feature now is soft-masking from left or right. This allows one to adjust
        a SAM record only by changing the cigar string to soft-mask a number of bases
        such that the rest of the SAM record (pos, tlen, etc.) remain valid, but
        downstream tools will not consider the soft-masked bases in further analysis.
        
        
        ```Python
        >>> from cigar import Cigar
        
        >>> c = Cigar('100M')
        >>> len(c)
        100
        >>> str(c)
        '100M'
        >>> list(c.items())
        [(100, 'M')]
        
        
        >>> c = Cigar('20H20M20S')
        >>> len(c)
        40
        >>> str(c)
        '20H20M20S'
        >>> list(c.items())
        [(20, 'H'), (20, 'M'), (20, 'S')]
        
        >>> c.mask_left(29).cigar, c.cigar
        ('20H9S11M20S', '20H20M20S')
        
        >>> c = Cigar('10M20S10M')
        >>> c.mask_left(10).cigar
        '30S10M'
        >>> c.mask_left(9).cigar
        '9S1M20S10M'
        >>> Cigar('10S').mask_left(10).cigar
        '10S'
        >>> Cigar('10H').mask_left(10).cigar
        '10H'
        >>> Cigar('10H').mask_left(11).cigar
        '10H'
        >>> Cigar('10H').mask_left(9).cigar
        '10H'
        
        >>> Cigar('1M10H').mask_left(9).cigar
        '1S10H'
        
        >>> Cigar('5M10H').mask_left(9).cigar
        '5S10H'
        
        >>> c = Cigar('1S1H1S5H1S5M10H')
        >>> c.mask_left(9).cigar == c.cigar
        True
        
        >>> c = Cigar('1S1H1S5H1S5M10H')
        >>> c.mask_right(9).cigar == c.cigar
        True
        >>> c.mask_right(11).cigar
        '1S1H1S5H1S4M1S10H'
        
        ```
        
        Installation
        ============
        
            pip install cigar
        
Platform: UNKNOWN
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 3
