# Efficient manipulation of CIGAR strings

## Documentation for package ‘cigarillo’ version 1.2.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package README

## Help Pages

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