Source code for modalysis.server.pileup

"""FastAPI routes for pileup operations."""

import logging

from fastapi import APIRouter

from modalysis.core import pileup as core_pileup
from modalysis.server.models import PileupFormatRequest, PileupMergeRequest

logger = logging.getLogger(__name__)

router = APIRouter(prefix="/pileup")




@router.post("/format")
def pileup_format(request: PileupFormatRequest) -> dict[str, str]:
    """Handle POST `/pileup/format` and run core pileup formatting."""
    logger.info("Server received pileup format request: %s", request)
    core_pileup.format(
        input_path=request.input_path,
        output_path=request.output_path,
        output_name=request.output_name,
        allowed_chromosomes=request.allowed_chromosomes,
    )
    return {"status": "success"}





@router.post("/merge")
def pileup_merge(request: PileupMergeRequest) -> dict[str, str]:
    """Handle POST `/pileup/merge` and run core pileup merging."""
    logger.info("Server received pileup merge request: %s", request)
    core_pileup.merge(
        pileup_paths=request.pileup_paths,
        output_path=request.output_path,
        output_name=request.output_name,
        min_files=request.min_files,
        min_file_coverage=request.min_file_coverage,
        min_reads=request.min_reads,
    )
    return {"status": "success"}