CRAM Index Management

Verifies that .crai index files exist for all input CRAMs, creating them with samtools index if missing. Required before any step that accesses specific genomic regions.

grid.utils.ensure_crai.ensure_crai(cram_path, reference=None)

Ensure a CRAI index exists for the given CRAM file.

Parameters:

• cram_path (str) – Path to CRAM file.

• reference (str) – Optional reference genome FASTA (required if CRAM is unindexed)

Returns:

Path to CRAI file.

Return type:

str