Efficient manipulation of CIGAR strings

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Documentation for package ‘cigarillo’ version 1.0.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

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cigarillo-package	Efficient manipulation of CIGAR strings
cigarillo	Efficient manipulation of CIGAR strings
cigars_as_ranges	Turn CIGAR strings into ranges of positions
cigars_as_ranges_along_pwa	Turn CIGAR strings into ranges of positions
cigars_as_ranges_along_query	Turn CIGAR strings into ranges of positions
cigars_as_ranges_along_ref	Turn CIGAR strings into ranges of positions
cigars_as_RleList	Explode CIGAR strings
cigar_extent	Calculate the number of positions spanned by a CIGAR string
cigar_extent_along_pwa	Calculate the number of positions spanned by a CIGAR string
cigar_extent_along_query	Calculate the number of positions spanned by a CIGAR string
cigar_extent_along_ref	Calculate the number of positions spanned by a CIGAR string
CIGAR_OPS	Visibility of CIGAR operations
cigar_ops_visibility	Visibility of CIGAR operations
explode_cigars	Explode CIGAR strings
explode_cigar_oplens	Explode CIGAR strings
explode_cigar_ops	Explode CIGAR strings
fast_map_ref_ranges_to_query	Map ranges relative to reference space to query space
map_ref_ranges_to_query	Map ranges relative to reference space to query space
narrow_cigars_along_query	Trim CIGAR strings along the reference or query space
narrow_cigars_along_ref	Trim CIGAR strings along the reference or query space
project_positions	Project positions from query to reference space and vice versa
project_sequences	Project sequences from one space to the other
query_pos_as_ref_pos	Project positions from query to reference space and vice versa
ref_pos_as_query_pos	Project positions from query to reference space and vice versa
tabulate_cigar_ops	Tabulate CIGAR operations
trim_cigars	Trim CIGAR strings along the reference or query space
trim_cigars_along_query	Trim CIGAR strings along the reference or query space
trim_cigars_along_ref	Trim CIGAR strings along the reference or query space
validate_cigars	Explode CIGAR strings