# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)

from spack.package import *


class Samtools(Package):
    """SAM Tools provide various utilities for manipulating alignments in
    the SAM format, including sorting, merging, indexing and generating
    alignments in a per-position format"""

    maintainers("jbeal-work")

    homepage = "https://www.htslib.org"
    url = "https://github.com/samtools/samtools/releases/download/1.13/samtools-1.13.tar.bz2"

    license("MIT")

    version("1.19", sha256="fa6b3b18e20851b6f3cb55afaf3205d02fcb79dae3b849fcf52e8fc10ff08b83")
    version("1.18", sha256="d686ffa621023ba61822a2a50b70e85d0b18e79371de5adb07828519d3fc06e1")
    version("1.17", sha256="3adf390b628219fd6408f14602a4c4aa90e63e18b395dad722ab519438a2a729")
    version("1.16.1", sha256="2fa0a25f78594cf23d07c9d32d5060a14f1c5ee14d7b0af7a8a71abc9fdf1d07")
    version("1.15.1", sha256="708c525ac76b0532b25f14aadea34a4d11df667bc19bf0a74dae617d80526c6e")
    version("1.15", sha256="35d945a5eee9817a764490870474f24e538400b0397b28f94247a5b91447215d")
    version("1.14", sha256="9341dabaa98b0ea7d60fd47e42af25df43a7d3d64d8e654cdf852974546b7d74")
    version("1.13", sha256="616ca2e051cc8009a1e9c01cfd8c7caf8b70916ddff66f3b76914079465f8c60")
    version("1.12", sha256="6da3770563b1c545ca8bdf78cf535e6d1753d6383983c7929245d5dba2902dcb")
    version("1.11", sha256="e283cebd6c1c49f0cf8a3ca4fa56e1d651496b4d2e42f80ab75991a9ece4e5b6")
    version("1.10", sha256="7b9ec5f05d61ec17bd9a82927e45d8ef37f813f79eb03fe06c88377f1bd03585")
    version("1.9", sha256="083f688d7070082411c72c27372104ed472ed7a620591d06f928e653ebc23482")
    version("1.8", sha256="c942bc1d9b85fd1b05ea79c5afd2805d489cd36b2c2d8517462682a4d779be16")
    version("1.7", sha256="e7b09673176aa32937abd80f95f432809e722f141b5342186dfef6a53df64ca1")
    version("1.6", sha256="ee5cd2c8d158a5969a6db59195ff90923c662000816cc0c41a190b2964dbe49e")
    version("1.5", sha256="8542da26832ee08c1978713f5f6188ff750635b50d8ab126a0c7bb2ac1ae2df6")
    version("1.4", sha256="9aae5bf835274981ae22d385a390b875aef34db91e6355337ca8b4dd2960e3f4")
    version("1.3.1", sha256="6c3d74355e9cf2d9b2e1460273285d154107659efa36a155704b1e4358b7d67e")
    version("1.2", sha256="420e7a4a107fe37619b9d300b6379452eb8eb04a4a9b65c3ec69de82ccc26daa")
    version(
        "0.1.8",
        sha256="343daf96f035c499c5b82dce7b4d96b10473308277e40c435942b6449853815b",
        url="https://github.com/samtools/samtools/archive/0.1.8.tar.gz",
    )

    depends_on("zlib-api")
    depends_on("ncurses")
    depends_on("perl", type="run")
    depends_on("python", type="run")

    # htslib became standalone @1.3.1, must use corresponding version
    depends_on("htslib@1.19", when="@1.19")
    depends_on("htslib@1.18", when="@1.18")
    depends_on("htslib@1.17", when="@1.17")
    depends_on("htslib@1.16", when="@1.16.1")
    depends_on("htslib@1.15.1", when="@1.15.1")
    depends_on("htslib@1.15", when="@1.15")
    depends_on("htslib@1.14", when="@1.14")
    depends_on("htslib@1.13", when="@1.13")
    depends_on("htslib@1.12", when="@1.12")
    depends_on("htslib@1.11", when="@1.11")
    depends_on("htslib@1.10.2", when="@1.10")
    depends_on("htslib@1.9", when="@1.9")
    depends_on("htslib@1.8", when="@1.8")
    depends_on("htslib@1.7", when="@1.7")
    depends_on("htslib@1.6", when="@1.6")
    depends_on("htslib@1.5", when="@1.5")
    depends_on("htslib@1.4", when="@1.4")
    depends_on("htslib@1.3.1", when="@1.3.1")

    def install(self, spec, prefix):
        if "+termlib" in spec["ncurses"]:
            curses_lib = "-lncursesw -ltinfow"
        else:
            curses_lib = "-lncursesw"

        if self.spec.version >= Version("1.3.1"):
            configure(
                "--prefix={0}".format(prefix),
                "--with-htslib={0}".format(self.spec["htslib"].prefix),
                "--with-ncurses",
                "CURSES_LIB={0}".format(curses_lib),
            )
            make()
            make("install")
        else:
            make("prefix={0}".format(prefix), "LIBCURSES={0}".format(curses_lib))
            if self.spec.version == Version("0.1.8"):
                make("prefix={0}".format(prefix))
            else:
                make("prefix={0}".format(prefix), "install")

        # Install dev headers and libs for legacy apps depending on them
        # per https://github.com/samtools/samtools/releases/tag/1.14
        # these have been removed (bam.h still exists but paired down)
        if spec.satisfies("@:1.13"):
            mkdir(prefix.include)
            mkdir(prefix.lib)
            install("sam.h", prefix.include)
            install("bam.h", prefix.include)
            install("libbam.a", prefix.lib)