cigarillo

cigarillo parses, inspects, trims, and converts CIGAR strings into query-space or reference-space position ranges, and projects positions or sequences between these spaces for BAM and AIRR-formatted alignment data.

Key Features:

• CIGAR String Parsing: Parses and inspects CIGAR strings from BAM files and AIRR-formatted IgBLAST output.
• CIGAR Trimming: Trims CIGAR strings to adjust alignment boundaries.
• Space Conversion: Converts CIGAR strings into ranges of positions relative to query space or reference space.
• Position Projection: Projects positions or sequences from query space to reference space and vice versa.
• Low-level Operations: Provides foundational operations typically used by higher-level packages such as GenomicAlignments and igblastr.

Scientific Applications:

• Alignment Analysis: Supports manipulation of gapped alignment data from sequence aligners producing BAM output.
• Immune Repertoire Analysis: Enables processing of AIRR-formatted CIGAR strings from IgBLAST for immunoglobulin and T-cell receptor sequence analysis.

Methodology:

The package implements low-level computational operations on CIGAR strings including parsing, trimming, conversion to position ranges in query or reference space, and bidirectional projection of positions and sequences between these spaces.