pandora_lib_promethion/setup-patches.ps1

param()
$ErrorActionPreference = "Stop"

$cargoDir = Join-Path $PSScriptRoot ".cargo"
if (-not (Test-Path $cargoDir)) {
    New-Item -ItemType Directory -Path $cargoDir | Out-Null
}
$cargoConfig = Join-Path $cargoDir "config.toml"
$cargoConfigText = @"
[patch.crates-io]
hts-sys = { path = "patches/hts-sys" }
rust-htslib = { path = "patches/rust-htslib" }
"@
[System.IO.File]::WriteAllText($cargoConfig, $cargoConfigText, (New-Object System.Text.UTF8Encoding $false))
Write-Host "Wrote local Windows Cargo patch config -> .cargo\config.toml"

$found = Resolve-Path "$env:USERPROFILE\.cargo\registry\src\index.crates.io-*\hts-sys-2.2.0" `
         -ErrorAction SilentlyContinue
if (-not $found) {
    Write-Error "hts-sys 2.2.0 not in cargo registry. Run 'cargo fetch' first."
    exit 1
}

$dest = Join-Path $PSScriptRoot "patches\hts-sys"
if (Test-Path $dest) { Remove-Item $dest -Recurse -Force }
Copy-Item $found.Path $dest -Recurse
Write-Host "Copied hts-sys 2.2.0 -> patches\hts-sys"

$buildRs = Join-Path $dest "build.rs"
$text = [System.IO.File]::ReadAllText($buildRs) -replace "`r`n", "`n"

# Fix 1: guard HAVE_DRAND48. drand48/srand48 are absent from MinGW libc.
$old1 = "    let mut config_lines = vec![`n        `"/* Default config.h generated by build.rs */`",`n        `"#define HAVE_DRAND48 1`",`n    ];"
$new1 = "    let mut config_lines = vec![`n        `"/* Default config.h generated by build.rs */`",`n    ];`n    if target_os != `"windows`" {`n        config_lines.push(`"#define HAVE_DRAND48 1`");`n    }"
$result = $text.Replace($old1, $new1)
if ($result -eq $text) { Write-Warning "Fix 1 pattern not matched - verify hts-sys version" }
else { Write-Host "Fix 1 applied (HAVE_DRAND48 guard)"; $text = $result }

# Fix 2: run version.sh through bash. Windows CreateProcess cannot execute .sh files.
$old2 = "        let version = std::process::Command::new(out.join(`"htslib`").join(`"version.sh`"))`n            .output()`n            .expect(`"failed to execute process`");`n        let version_str = std::str::from_utf8(&version.stdout).unwrap().trim();"
$new2 = "        let version_str = std::process::Command::new(`"bash`")`n            .arg(out.join(`"htslib`").join(`"version.sh`"))`n            .output()`n            .map(|o| std::str::from_utf8(&o.stdout).unwrap_or(`"1.19.1`").trim().to_string())`n            .unwrap_or_else(|_| `"1.19.1`".to_string());"
$result = $text.Replace($old2, $new2)
if ($result -eq $text) { Write-Warning "Fix 2 pattern not matched - verify hts-sys version" }
else { Write-Host "Fix 2 applied (version.sh via bash)"; $text = $result }

# Fix 3: 64-bit file offsets on Windows MinGW.
# Both the C compiler and bindgen must see the same define so types match.
$old3 = "    if want_static {`n        cfg.warnings(false).static_flag(true).pic(true);`n    } else {`n        cfg.warnings(false).static_flag(false).pic(true);`n    }"
$new3 = "    if want_static {`n        cfg.warnings(false).static_flag(true).pic(true);`n    } else {`n        cfg.warnings(false).static_flag(false).pic(true);`n    }`n`n    // Fix 3: 64-bit file offsets on Windows MinGW.`n    // Without this, off_t = i32 and seeks wrap at 2 GB.`n    if target_os == `"windows`" {`n        cfg.define(`"_FILE_OFFSET_BITS`", `"64`");`n    }"
$result = $text.Replace($old3, $new3)
if ($result -eq $text) { Write-Warning "Fix 3a pattern not matched - verify hts-sys version" }
else { Write-Host "Fix 3a applied (_FILE_OFFSET_BITS=64 cc define)"; $text = $result }

$old4 = "        bindgen::Builder::default()`n            .header(`"wrapper.h`")`n            .generate_comments(false)`n            .blocklist_function(`"strtold`")`n            .blocklist_type(`"max_align_t`")`n            .generate()"
$new4 = "        let mut bindgen_builder = bindgen::Builder::default()`n            .header(`"wrapper.h`")`n            .generate_comments(false)`n            .blocklist_function(`"strtold`")`n            .blocklist_type(`"max_align_t`");`n        if target_os == `"windows`" {`n            bindgen_builder = bindgen_builder.clang_arg(`"-D_FILE_OFFSET_BITS=64`");`n        }`n        bindgen_builder`n            .generate()"
$result = $text.Replace($old4, $new4)
if ($result -eq $text) { Write-Warning "Fix 3b pattern not matched - verify hts-sys version" }
else { Write-Host "Fix 3b applied (_FILE_OFFSET_BITS=64 bindgen)"; $text = $result }

# Fix 4: static-link MinGW regex libraries on Windows.
# hts_expr.c needs POSIX regex; systre.c needs TRE. libregex depends on
# libintl/gettext, which depends on libiconv.
$old5 = "    cfg.file(`"wrapper.c`");`n    cfg.compile(`"hts`");"
$new5 = "    cfg.file(`"wrapper.c`");`n    cfg.compile(`"hts`");`n`n    // hts_expr.c uses POSIX regex (regcomp/regexec/regfree) -- provided by libregex (gnurx).`n    // systre.c uses the TRE regex API (tre_regexec/tre_regerror) -- provided by libtre.`n    // Both live in the MinGW lib dir; locate it via gcc -print-file-name.`n    // Link statically so the exe has no runtime dependency on .dll files.`n    if target_os == `"windows`" {`n        let compiler = cfg.get_compiler();`n        let mingw_lib = std::process::Command::new(compiler.path())`n            .arg(`"-print-file-name=libtre.a`")`n            .output()`n            .ok()`n            .and_then(|o| String::from_utf8(o.stdout).ok())`n            .map(|s| s.trim().to_string())`n            .filter(|s| s != `"libtre.a`")`n            .and_then(|s| std::path::PathBuf::from(s).parent().map(|p| p.to_path_buf()));`n        if let Some(dir) = mingw_lib {`n            println!(`"cargo:rustc-link-search=native={}`", dir.display());`n        }`n        println!(`"cargo:rustc-link-lib=dylib:+verbatim=libcurl.dll.a`"); // hfile_libcurl.c: curl_easy/curl_multi APIs`n        println!(`"cargo:rustc-link-lib=static=tre`");    // systre.c: tre_regexec/tre_regerror`n        println!(`"cargo:rustc-link-lib=static=regex`");  // hts_expr.c: regcomp/regexec/regfree`n        println!(`"cargo:rustc-link-lib=static=intl`");   // libregex dep: gettext`n        println!(`"cargo:rustc-link-lib=static=iconv`");  // libintl dep: iconv`n    }"
$result = $text.Replace($old5, $new5)
if ($result -eq $text) { Write-Warning "Fix 4 pattern not matched - verify hts-sys version" }
else { Write-Host "Fix 4 applied (static-link regex/tre/intl/iconv on Windows)"; $text = $result }

[System.IO.File]::WriteAllText($buildRs, $text, (New-Object System.Text.UTF8Encoding $false))

$cargoToml = Join-Path $dest "Cargo.toml"
$manifest = [System.IO.File]::ReadAllText($cargoToml) -replace "`r`n", "`n"
$oldManifest = "[target.'cfg(all(unix, not(target_os = `"macos`")))'.dependencies.openssl-sys]`nversion = `"0.9.56`"`noptional = true"
$newManifest = "[target.'cfg(any(windows, all(unix, not(target_os = `"macos`"))))'.dependencies.openssl-sys]`nversion = `"0.9.56`"`noptional = true"
$result = $manifest.Replace($oldManifest, $newManifest)
if ($result -eq $manifest) { Write-Warning "Manifest OpenSSL target patch not matched - verify hts-sys version" }
else {
    Write-Host "Manifest patch applied (openssl-sys enabled on Windows)"
    [System.IO.File]::WriteAllText($cargoToml, $result, (New-Object System.Text.UTF8Encoding $false))
}

Write-Host "patches\hts-sys is ready."

$rhl = Resolve-Path "$env:USERPROFILE\.cargo\registry\src\index.crates.io-*\rust-htslib-1.0.0" `
       -ErrorAction SilentlyContinue
if (-not $rhl) {
    Write-Warning "rust-htslib 1.0.0 not in cargo registry. Run 'cargo fetch' first."
} else {
    $rhlDest = Join-Path $PSScriptRoot "patches\rust-htslib"
    if (Test-Path $rhlDest) { Remove-Item $rhlDest -Recurse -Force }
    Copy-Item $rhl.Path $rhlDest -Recurse
    Write-Host "Copied rust-htslib 1.0.0 -> patches\rust-htslib"

    $bamMod = Join-Path $rhlDest "src\bam\mod.rs"
    $rhlText = [System.IO.File]::ReadAllText($bamMod) -replace "`r`n", "`n"

    $rhlText = $rhlText.Replace("offset as libc::off_t,", "offset as hts_sys::off_t,")
    if ($rhlText -match "offset as libc::off_t") {
        Write-Warning "rust-htslib fix A not applied - pattern not matched"
    } else {
        Write-Host "rust-htslib fix A applied (libc::off_t -> hts_sys::off_t)"
    }

    $oldIdxLoad = "        let idx = unsafe { htslib::sam_index_load(htsfile, c_str.as_ptr()) };"
    $newIdxLoad = "        // flags=0 omits HTS_IDX_SAVE_REMOTE so remote .bai files are not cached locally.`n        let idx = unsafe { htslib::sam_index_load3(htsfile, c_str.as_ptr(), std::ptr::null(), 0) };"
    $rhlText = $rhlText.Replace($oldIdxLoad, $newIdxLoad)
    if ($rhlText -match "sam_index_load\(htsfile") {
        Write-Warning "rust-htslib fix B not applied - pattern not matched"
    } else {
        Write-Host "rust-htslib fix B applied (sam_index_load3 no-cache)"
    }

    $fromUrl = "    pub fn from_url(url: &Url) -> Result<Self> {`n        Self::new(url.as_str().as_bytes())`n    }"
    $fromUrlAndIndex = "    pub fn from_url(url: &Url) -> Result<Self> {`n        Self::new(url.as_str().as_bytes())`n    }`n`n    /// Open a remote BAM via URL with a pre-downloaded local index file.`n    /// Using a local index bypasses htslib's remote-index caching entirely.`n    pub fn from_url_and_index<P: AsRef<Path>>(url: &Url, index_path: P) -> Result<Self> {`n        Self::new_with_index_path(`n            url.as_str().as_bytes(),`n            &path_as_bytes(index_path, true)?,`n        )`n    }"
    $count = ([regex]::Matches($rhlText, [regex]::Escape($fromUrl))).Count
    if ($count -ge 2) {
        $idx = $rhlText.IndexOf($fromUrl, $rhlText.IndexOf($fromUrl) + 1)
        $rhlText = $rhlText.Substring(0, $idx) + $fromUrlAndIndex + $rhlText.Substring($idx + $fromUrl.Length)
        Write-Host "rust-htslib fix C applied (IndexedReader::from_url_and_index)"
    } else {
        Write-Warning "rust-htslib fix C not applied - could not locate second from_url in IndexedReader"
    }

    [System.IO.File]::WriteAllText($bamMod, $rhlText, (New-Object System.Text.UTF8Encoding $false))
    Write-Host "patches\rust-htslib is ready."
}