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.

>>> 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
conda install -c bioconda cigar