FlattenCigar¶

The "flattenCigar" transform expands an alignment row into one row per CIGAR operation. It is intended for BAM alignment visualizations where aligned blocks, insertions, deletions, skipped regions, and clipped ends need separate marks. For background on the CIGAR notation, see the SAM/BAM format specification.

The transform preserves the input fields, or only the fields listed in copyFields when it is defined, and adds:

Reference coordinates are 0-based and half-open. Insertions and clipped bases are emitted as zero-width reference-anchored rows. Unavailable CIGAR values (*) produce no rows.

The copyFields parameter limits which top-level input fields are copied to the emitted operation rows. For example, BAM reads often contain long sequence and base-quality fields that are needed upstream but not in CIGAR overlay rows.

Parameters¶

cigar

Type: string (field name)

The CIGAR string.

Default value: "cigar"

copyFields

Type: array

Top-level input fields copied to the emitted CIGAR operation rows.

If omitted, all input fields are copied. This can be used to avoid copying bulky fields such as read sequence or base quality arrays while still allowing the transform to read its input fields.

description

Type: string

A description of the transform step. Can be used for documentation and agent context.

start

Type: string (field name)

The read's reference start coordinate.

Default value: "start"

Example¶

Given the following data:

... and configuration:

{
  "type": "flattenCigar"
}

The CIGAR operations are expanded into new data objects. The original fields are preserved:

Layers can filter by cigarType and render different operation types with ordinary marks.

For a complete genomic visualization example, see BAM Read Alignments.