#!/usr/bin/env python3
"""
This script can be symlinked to samtools, bcftools, bgzip, or tabix.
When invoked under one of those names, it will emulate that tool's
behaviour by using pysam's facilities.
"""

import argparse
import gzip
import os
import sys
import tempfile

import pysam

command = os.path.basename(sys.argv[0])

if command in ("samtools", "bcftools"):
    if len(sys.argv) > 1:
        try:
            tool = pysam.utils.PysamDispatcher(command, sys.argv[1])
            tool(*sys.argv[2:], catch_stdout=None)
            print(tool.stderr, end="", file=sys.stderr)
        except pysam.utils.SamtoolsError as e:
            sys.exit(f"emulate-tools.py: {e}")

    else:
        version = getattr(pysam.version, f"__{command}_version__")
        print(f"Program: {command}\nVersion: {version}", file=sys.stderr)

else:
    parser = argparse.ArgumentParser()
    parser.add_argument("-c", "--stdout", action="store_true")
    parser.add_argument("-d", "--decompress", action="store_true")
    parser.add_argument("-f", "--force", action="store_true")
    parser.add_argument("-p", "--preset")
    parser.add_argument("input_file", nargs="?")
    opt = parser.parse_args()

    if command == "bgzip":
        if opt.decompress:
            with gzip.open(sys.stdin.buffer, "rb") as f:
                sys.stdout.buffer.write(f.read())

        elif opt.input_file and opt.stdout:
            pysam.tabix_compress(opt.input_file, "-", force=True)

        else:
            f = tempfile.NamedTemporaryFile(delete=False)
            f.write(sys.stdin.buffer.read())
            f.close()
            pysam.tabix_compress(f.name, "-", force=True)
            os.remove(f.name)

    elif command == "tabix":
        pysam.tabix_index(opt.input_file, preset=opt.preset, force=opt.force)

    else:
        sys.exit(f"emulate-tools.py: unknown command {command!r}")