precellar.Assay.update_read

Assay.update_read(read_id, *, modality=None, primer_id=None, is_reverse=None, fastq=None, min_len=None, max_len=None, compute_md5=False, infer_read_length=True, infer_read_length_sample=1000)

Update read information in the Assay object.

This method updates the read information in the Assay object. If the read does not exist, it will be created.

Parameters:

• read_id (str) – The id of the read.

• modality (str | None) – The modality of the read.

• primer_id (str | None) – The id of the primer.

• is_reverse (bool | None) – Whether the read is reverse.

• fastq (Path | list[Path] | None) – The path to the fastq file containing the reads. It can be: (1) a single path, or (2) a list of paths, or (3) a glob pattern, e.g., *.fastq.

• min_len (int | None) – The minimum length of the read. If not provided, the minimum length is inferred from the fastq file.

• max_len (int | None) – The maximum length of the read. If not provided, the maximum length is inferred from the fastq file.

• compute_md5 (bool) – Whether to compute the md5 hash of the fastq file.

• infer_read_length (bool) – Whether to infer the read length from the fastq file.

• infer_read_length_sample (int | None) – The number of records to sample from the fastq file to infer the read length.