BAM Format

Stream BAM (Binary Alignment/Map) alignments as one record per read.

Overview

Property	Value
Format id	bam
Class	BAMIterable
Extensions	.bam
Read	Yes
Write	No
Extra	alignment (pysam)
Maturity	stable

Record shape

{
    "query_name": "read1",
    "flag": 0,
    "reference_id": 0,
    "reference_start": 100,
    "mapping_quality": 60,
    "cigarstring": "50M",
    "next_reference_id": -1,
    "next_reference_start": -1,
    "template_length": 0,
    "query_sequence": "ACGT...",
    "query_qualities": "IIII...",
}

Requires a filename (streams not supported).

Usage

from iterable import open_iterable

with open_iterable("alignments.bam", format="bam") as source:
    for aln in source:
        print(aln["query_name"], aln["reference_start"], aln["cigarstring"])

Install with pip install iterabledata[alignment].

See also

• SAM — text Sequence Alignment/Map
• Supported formats