apcamargo

#!/usr/bin/env python

"""
This script processes SAM (Sequence Alignment/Map format) inputs from standard
input and extracts alignment information that is then provided in a tab-separated
table. The following fields are produced: query, target, query_length, query_start,
query_end, target_start, target_end, alignment_length, alignment_identity.

This script was designed for use with SAM files produced by minimap2. However,
it will work with any SAM data that:

apcamargo

from pathlib import Path
from typing import Iterator, Optional, Union

import polars as pl
from needletail import parse_fastx_file
from polars.io.plugins import register_io_source


def scan_fastx(fastx_file: Union[str, Path]) -> pl.LazyFrame:
    schema = pl.Schema(