Sweep: update snps about php-dna

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php-dna/src/Snps/SNPs.php

Lines 1 to 694 in 87b5cd2

	<?php
	namespace Dna\Snps;
	use Countable;
	use Dna\Resources;
	use Dna\Snps\IO\IO;
	use Dna\Snps\IO\Reader;
	use Dna\Snps\IO\Writer;
	use Iterator;
	// You may need to find alternative libraries for numpy, pandas, and snps in PHP, as these libraries are specific to Python
	// For numpy, consider using a library such as MathPHP: https://github.com/markrogoyski/math-php
	// For pandas, you can use DataFrame from https://github.com/aberenyi/php-dataframe, though it is not as feature-rich as pandas
	// For snps, you'll need to find a suitable PHP alternative or adapt the Python code to PHP
	// import copy // In PHP, you don't need to import the 'copy' module, as objects are automatically copied when assigned to variables
	// from itertools import groupby, count // PHP has built-in support for array functions that can handle these operations natively
	// import logging // For logging in PHP, you can use Monolog: https://github.com/Seldaek/monolog
	// use Monolog\Logger;
	// use Monolog\Handler\StreamHandler;
	// import os, re, warnings
	// PHP has built-in support for file operations, regex, and error handling, so no need to import these modules
	// import numpy as np // See the note above about using MathPHP or another PHP library for numerical operations
	// import pandas as pd // See the note above about using php-dataframe or another PHP library for data manipulation
	// from pandas.api.types import CategoricalDtype // If using php-dataframe, check documentation for similar functionality
	// For snps.ensembl, snps.resources, snps.io, and snps.utils, you'll need to find suitable PHP alternatives or adapt the Python code
	use Dna\Snps\Ensembl;
	use Dna\Snps\IO\SnpFileReader;
	use Dna\Snps\Analysis\BuildDetector;
	use Dna\Snps\Analysis\ClusterOverlapCalculator;
	// from snps.utils import Parallelizer
	// Set up logging
	// $logger = new Logger('my_logger');
	// $logger->pushHandler(new StreamHandler('php://stderr', Logger::DEBUG));
	class SNPs implements Countable, Iterator
	{
	private array $_source = [];
	private array $_snps = [];
	private int $_build = 0;
	private ?bool $_phased = null;
	private ?bool $_build_detected = null;
	private ?Resources $_resources = null;
	private ?string $_chip = null;
	private ?string $_chip_version = null;
	private ?string $_cluster = null;
	private int $_position = 0;
	private array $_keys = [];
	private array $_duplicate;
	private array $_discrepant_XY;
	private array $_heterozygous_MT;
	private $_chip;
	private $_chip_version;
	private $_cluster;
	/**
	* SNPs constructor.
	*
	* @param string $file Input file path
	* @param bool $only_detect_source Flag to indicate whether to only detect the source
	* @param bool $assign_par_snps Flag to indicate whether to assign par_snps
	* @param string $output_dir Output directory path
	* @param string $resources_dir Resources directory path
	* @param bool $deduplicate Flag to indicate whether to deduplicate
	* @param bool $deduplicate_XY_chrom Flag to indicate whether to deduplicate XY chromosome
	* @param bool $deduplicate_MT_chrom Flag to indicate whether to deduplicate MT chromosome
	* @param bool $parallelize Flag to indicate whether to parallelize
	* @param int $processes Number of processes to use for parallelization
	* @param array $rsids Array of rsids
	*/
	public function __construct(
	private $file = "",
	private bool $only_detect_source = False,
	private bool $assign_par_snps = False,
	private string $output_dir = "output",
	private string $resources_dir = "resources",
	private bool $deduplicate = True,
	private bool $deduplicate_XY_chrom = True,
	private bool $deduplicate_MT_chrom = True,
	private bool $parallelize = False,
	private int $processes = 1, // cpu count
	private array $rsids = [],
	private $ensemblRestClient = null,
	) //, $only_detect_source, $output_dir, $resources_dir, $parallelize, $processes)
	{
	// $this->_only_detect_source = $only_detect_source;
	$this->snpFileReader = new SnpFileReader($this->_resources, $this->ensemblRestClient);
	$this->buildDetector = new BuildDetector();
	$this->clusterOverlapCalculator = new ClusterOverlapCalculator($this->_resources);
	$this->_source = [];
	$this->_phased = null;
	$this->_build = 0;
	$this->_build_detected = null;
	$this->_cluster = "";
	$this->_chip = "";
	$this->_chip_version = "";
	$this->_source = [];
	// $this->_phased = false;
	$this->_build = 0;
	$this->_build_detected = false;
	// $this->_output_dir = $output_dir;
	$this->_resources = new Resources($resources_dir);
	// $this->_parallelizer = new Parallelizer($parallelize, $processes);
	$this->_cluster = "";
	$this->_chip = "";
	$this->_chip_version = "";
	$this->ensemblRestClient = $ensemblRestClient ?? new Ensembl("https://api.ncbi.nlm.nih.gov", 1);
	if (!empty($file)) {
	$this->readFile();
	}
	}
	public function count(): int
	{
	return $this->get_count();
	}
	public function current(): SNPs
	{
	return $this->_snps[$this->_position];
	}
	public function key(): int
	{
	return $this->_position;
	}
	public function next(): void
	{
	++$this->_position;
	}
	public function rewind(): void
	{
	$this->_position = 0;
	}
	public function valid(): bool
	{
	return isset($this->_snps[$this->_position]);
	}
	/**
	* Get the SNPs as a DataFrame.
	*
	* @return SNPs[] The SNPs array
	*/
	public function filter(callable $callback)
	{
	return array_filter($this->_snps, $callback);
	}
	/**
	* Get the value of the source property.
	*
	* @return string
	* Data source(s) for this `SNPs` object, separated by ", ".
	*/
	public function getSource(): string
	{
	return implode(", ", $this->_source);
	}
	public function getAllSources(): array
	{
	return $this->_source;
	}
	/**
	* Magic method to handle property access.
	*
	* @param string $name
	* The name of the property.
	*
	* @return mixed
	* The value of the property.
	*/
	public function __get(string $name)
	{
	$getter = 'get' . ucfirst($name);
	if (method_exists($this, $getter)) {
	return $this->$getter();
	}
	return null; // Or throw an exception for undefined properties
	}
	public function setSNPs(array $snps)
	{
	$this->_snps = $snps;
	$this->_keys = array_keys($snps);
	}
	// Method readFile has been removed and its functionality is refactored with SnpFileReader class
	$this->setSNPs($d["snps"]);
	$this->_source = (strpos($d["source"], ", ") !== false) ? explode(", ", $d["source"]) : [$d["source"]];
	$this->_phased = $d["phased"];
	$this->_build = $d["build"] ?? null;
	$this->_build_detected = !empty($d["build"]);
	// echo "HERE\n";
	// var_dump($d["build"]);
	// var_dump($this->_build_detected);
	// $this->_cluster = $d["cluster"];
	// if not self._snps.empty:
	// self.sort()
	// if deduplicate:
	// self._deduplicate_rsids()
	// # use build detected from `read` method or comments, if any
	// # otherwise use SNP positions to detect build
	// if not self._build_detected:
	// self._build = self.detect_build()
	// self._build_detected = True if self._build else False
	// if not self._build:
	// self._build = 37 # assume Build 37 / GRCh37 if not detected
	// else:
	// self._build_detected = True
	if (!empty($this->_snps)) {
	$this->sort();
	if ($this->deduplicate)
	$this->_deduplicate_rsids();
	// use build detected from `read` method or comments, if any
	// otherwise use SNP positions to detect build
	if (!$this->_build_detected) {
	$this->_build = $this->detect_build();
	$this->_build_detected = $this->_build ? true : false;
	if (!$this->_build) {
	$this->_build = 37; // assume Build 37 / GRCh37 if not detected
	} else {
	$this->_build_detected = true;
	}
	}
	// if ($this->assign_par_snps) {
	// $this->assignParSnps();
	// $this->sort();
	// }
	// if ($this->deduplicate_XY_chrom) {
	// if (
	// ($this->deduplicate_XY_chrom === true && $this->determine_sex() == "Male")
	// || ($this->determine_sex(chrom: $this->deduplicate_XY_chrom) == "Male")
	// ) {
	// $this->deduplicate_XY_chrom();
	// }
	// }
	// if ($this->deduplicate_MT_chrom) {
	// echo "deduping yo...\n";
	// $this->deduplicate_MT_chrom();
	// }
	}
	}
	// Method readRawData has been removed and its functionality is refactored with SnpFileReader class
	}
	/**
	* Get the SNPs as an array.
	*
	* @return array The SNPs array
	*/
	public function getSnps(): array
	{
	return $this->_snps;
	}
	/**
	* Status indicating if build of SNPs was detected.
	*
	* @return bool True if the build was detected, False otherwise
	*/
	public function isBuildDetected(): bool
	{
	return $this->_build_detected;
	}
	/**
	* Get the build number associated with the data.
	*
	* @return mixed The build number
	*/
	public function getBuild()
	{
	return $this->_build;
	}
	public function setBuild($build)
	{
	$this->_build = $build;
	}
	/**
	* Detected deduced genotype / chip array, if any, per computeClusterOverlap.
	*
	* @return string Detected chip array, else an empty string.
	*/
	public function getChip()
	{
	if (empty($this->_chip)) {
	$this->computeClusterOverlap();
	}
	return $this->_chip;
	}
	/**
	* Detected genotype / chip array version, if any, per
	* computeClusterOverlap.
	*
	* Chip array version is only applicable to 23andMe (v3, v4, v5) and AncestryDNA (v1, v2) files.
	*
	* @return string Detected chip array version, e.g., 'v4', else an empty string.
	*/
	public function getChipVersion()
	{
	if (!$this->_chip_version) {
	$this->computeClusterOverlap();
	}
	return $this->_chip_version;
	}
	/**
	* Compute overlap with chip clusters.
	*
	* Chip clusters, which are defined in [1]_, are associated with deduced genotype /
	* chip arrays and DTC companies.
	*
	* This method also sets the values returned by the `cluster`, `chip`, and
	* `chip_version` properties, based on max overlap, if the specified threshold is
	* satisfied.
	*
	* @param float $clusterOverlapThreshold
	* Threshold for cluster to overlap this SNPs object, and vice versa, to set
	* values returned by the `cluster`, `chip`, and `chip_version` properties.
	*
	* @return array
	* Associative array with the following keys:
	* - `companyComposition`: DTC company composition of associated cluster from [1]_
	* - `chipBaseDeduced`: Deduced genotype / chip array of associated cluster from [1]_
	* - `snpsInCluster`: Count of SNPs in cluster
	* - `snpsInCommon`: Count of SNPs in common with cluster (inner merge with cluster)
	* - `overlapWithCluster`: Percentage overlap of `snpsInCommon` with cluster
	* - `overlapWithSelf`: Percentage overlap of `snpsInCommon` with this SNPs object
	*
	* @see https://doi.org/10.1016/j.csbj.2021.06.040
	* Chang Lu, Bastian Greshake Tzovaras, Julian Gough, A survey of
	* direct-to-consumer genotype data, and quality control tool
	* (GenomePrep) for research, Computational and Structural
	* Biotechnology Journal, Volume 19, 2021, Pages 3747-3754, ISSN
	* 2001-0370.
	*/
	// Method computeClusterOverlap has been removed and its functionality is refactored with ClusterOverlapCalculator class
	];
	$keys = array_keys($data);
	$df = [];
	foreach ($data['cluster_id'] as $index => $cluster_id) {
	$entry = ['cluster_id' => $cluster_id];
	foreach ($keys as $key) {
	$entry[$key] = $data[$key][$index];
	}
	$df[] = $entry;
	}
	if ($this->build != 37) {
	// Create a deep copy of the current object
	$toRemap = clone $this;
	// Call the remap method on the copied object
	$toRemap->remap(37); // clusters are relative to Build 37
	// Extract "chrom" and "pos" values from snps and remove duplicates
	$selfSnps = [];
	foreach ($toRemap->snps as $snp) {
	if (
	!in_array($snp["chrom"], array_column($selfSnps, "chrom")) ||
	!in_array($snp["pos"], array_column($selfSnps, "pos"))
	) {
	$selfSnps[] = $snp;
	}
	}
	} else {
	// Extract "chrom" and "pos" values from snps and remove duplicates
	$selfSnps = [];
	foreach ($this->snps as $snp) {
	if (
	!in_array($snp["chrom"], array_column($selfSnps, "chrom")) ||
	!in_array($snp["pos"], array_column($selfSnps, "pos"))
	) {
	$selfSnps[] = $snp;
	}
	}
	}
	$chip_clusters = $this->_resources->get_chip_clusters();
	foreach ($df as $cluster => $row) {
	$cluster_snps = array_filter($chip_clusters, function ($chip_cluster) use ($cluster) {
	return strpos($chip_cluster['clusters'], $cluster) !== false;
	});
	$df[$cluster]["snps_in_cluster"] = count($cluster_snps);
	$df[$cluster]["snps_in_common"] = count(array_uintersect($selfSnps, $cluster_snps, function ($a, $b) {
	return $a["chrom"] == $b["chrom"] && $a["pos"] == $b["pos"] ? 0 : 1;
	}));
	}
	foreach ($df as &$row) {
	$row["overlap_with_cluster"] = $row["snps_in_common"] / $row["snps_in_cluster"];
	$row["overlap_with_self"] = $row["snps_in_common"] / count($selfSnps);
	}
	$max_overlap = array_keys($df, max($df))[0];
	if (
	$df["overlap_with_cluster"][$max_overlap] > $cluster_overlap_threshold
	&& $df["overlap_with_self"][$max_overlap] > $cluster_overlap_threshold
	) {
	$this->_cluster = $max_overlap;
	$this->_chip = $df["chip_base_deduced"][$max_overlap];
	$company_composition = $df["company_composition"][$max_overlap];
	if ($this->source === "23andMe" || $this->source === "AncestryDNA") {
	$i = strpos($company_composition, "v");
	if ($i !== false) {
	$this->_chip_version = substr($company_composition, $i, 2);
	}
	} else {
	error_log("Detected SNPs data source not found in cluster's company composition");
	}
	}
	return $df;
	}
	/**
	* Discrepant XY SNPs.
	*
	* Discrepant XY SNPs are SNPs that are assigned to both the X and Y chromosomes.
	*
	* @return array Discrepant XY SNPs
	*/
	public function getDiscrepantXY()
	{
	return $this->_discrepant_XY;
	}
	/**
	* Get the duplicate SNPs.
	*
	* A duplicate SNP has the same RSID as another SNP. The first occurrence
	* of the RSID is not considered a duplicate SNP.
	*
	* @return SNPs[] Duplicate SNPs
	*/
	public function getDuplicate()
	{
	return $this->_duplicate;
	}
	/**
	* Count of SNPs.
	*
	* @param string $chrom (optional) Chromosome (e.g., "1", "X", "MT")
	* @return int The count of SNPs for the given chromosome
	*/
	public function get_count($chrom = "")
	{
	return count($this->_filter($chrom));
	}
	protected function _filter($chrom = "")
	{
	if (!empty($chrom)) {
	$filteredSnps = array_filter($this->_snps, function ($snp) use ($chrom) {
	return $snp['chrom'] === $chrom;
	});
	return $filteredSnps;
	} else {
	return $this->_snps;
	}
	}
	/**
	* Detect build of SNPs.
	*
	* Use the coordinates of common SNPs to identify the build / assembly of a genotype file
	* that is being loaded.
	*
	* Notes:
	* - rs3094315 : plus strand in 36, 37, and 38
	* - rs11928389 : plus strand in 36, minus strand in 37 and 38
	* - rs2500347 : plus strand in 36 and 37, minus strand in 38
	* - rs964481 : plus strand in 36, 37, and 38
	* - rs2341354 : plus strand in 36, 37, and 38
	* - rs3850290 : plus strand in 36, 37, and 38
	* - rs1329546 : plus strand in 36, 37, and 38
	*
	* Returns detected build of SNPs, else 0
	*
	* References:
	* 1. Yates et. al. (doi:10.1093/bioinformatics/btu613),
	* <http://europepmc.org/search/?query=DOI:10.1093/bioinformatics/btu613>
	* 2. Zerbino et. al. (doi.org/10.1093/nar/gkx1098), https://doi.org/10.1093/nar/gkx1098
	* 3. Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K.
	* dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001
	* Jan 1;29(1):308-11.
	* 4. Database of Single Nucleotide Polymorphisms (dbSNP). Bethesda (MD): National Center
	* for Biotechnology Information, National Library of Medicine. dbSNP accession: rs3094315,
	* rs11928389, rs2500347, rs964481, rs2341354, rs3850290, and rs1329546
	* (dbSNP Build ID: 151). Available from: http://www.ncbi.nlm.nih.gov/SNP/
	*/
	// Method detect_build has been removed and its functionality is refactored with BuildDetector class
	"rs3850290",
	"rs1329546",
	];
	$df = [
	"rs3094315" => [36 => 742429, 37 => 752566, 38 => 817186],
	"rs11928389" => [36 => 50908372, 37 => 50927009, 38 => 50889578],
	"rs2500347" => [36 => 143649677, 37 => 144938320, 38 => 148946169],
	"rs964481" => [36 => 27566744, 37 => 27656823, 38 => 27638706],
	"rs2341354" => [36 => 908436, 37 => 918573, 38 => 983193],
	"rs3850290" => [36 => 22315141, 37 => 23245301, 38 => 22776092],
	"rs1329546" => [36 => 135302086, 37 => 135474420, 38 => 136392261]
	];
	foreach ($this->_snps as $snp) {
	if (in_array($snp['rsid'], $rsids)) {
	$build = $lookup_build_with_snp_pos($snp['pos'], $df[$snp['rsid']]);
	}
	if ($build) {
	break;
	}
	}
	return $build;
	}
	/**
	* Convert the SNPs object to a string representation.
	*
	* @return string The string representation of the SNPs object
	*/
	public function __toString()
	{
	if (is_string($this->file) && is_file($this->file)) {
	// If the file path is a string, return SNPs with the basename of the file
	return "SNPs('" . basename($this->file) . "')";
	} else {
	// If the file path is not a string, return SNPs with <bytes>
	return "SNPs(<bytes>)";
	}
	}
	/**
	* Get the assembly of the SNPs.
	*
	* @return string The assembly of the SNPs
	*/
	public function getAssembly(): string
	{
	if ($this->_build === 37) {
	return "GRCh37";
	} elseif ($this->_build === 36) {
	return "NCBI36";
	} elseif ($this->_build === 38) {
	return "GRCh38";
	} else {
	return "";
	}
	}
	/**
	* Assign PAR SNPs to the X or Y chromosome using SNP position.
	*
	* References:
	* 1. National Center for Biotechnology Information, Variation Services, RefSNP,
	* https://api.ncbi.nlm.nih.gov/variation/v0/
	* 2. Yates et. al. (doi:10.1093/bioinformatics/btu613),
	* http://europepmc.org/search/?query=DOI:10.1093/bioinformatics/btu613
	* 3. Zerbino et. al. (doi.org/10.1093/nar/gkx1098), https://doi.org/10.1093/nar/gkx1098
	* 4. Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K.
	* dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;
	* 29(1):308-11.
	* 5. Database of Single Nucleotide Polymorphisms (dbSNP). Bethesda (MD): National Center
	* for Biotechnology Information, National Library of Medicine. dbSNP accession:
	* rs28736870, rs113313554, and rs758419898 (dbSNP Build ID: 151). Available from:
	* http://www.ncbi.nlm.nih.gov/SNP/
	*/
	protected function assignParSnps()
	{
	$restClient = $this->ensemblRestClient;
	$snps = $this->filter(function ($snps) {
	return $snps["chrom"] === "PAR";
	});
	foreach ($snps as $snp) {
	$rsid = $snp["rsid"];
	echo "rsid: $rsid\n";
	if (str_starts_with($rsid, "rs")) {
	$response = $this->lookupRefsnpSnapshot($rsid, $restClient);
	// print_r($response);
	if ($response !== null) {
	// print_r($response["primary_snapshot_data"]["placements_with_allele"]);
	foreach ($response["primary_snapshot_data"]["placements_with_allele"] as $item) {
	// print_r($item["seq_id"]);
	// var_dump(str_starts_with($item["seq_id"], "NC_000023"));
	// var_dump(str_starts_with($item["seq_id"], "NC_000024"));
	if (str_starts_with($item["seq_id"], "NC_000023")) {
	$assigned = $this->assignSnp($rsid, $item["alleles"], "X");
	// var_dump($assigned);
	} elseif (str_starts_with($item["seq_id"], "NC_000024")) {
	$assigned = $this->assignSnp($rsid, $item["alleles"], "Y");
	// var_dump($assigned);
	} else {
	$assigned = false;
	}
	if ($assigned) {
	if (!$this->_build_detected) {
	$this->_build = $this->extractBuild($item);
	$this->_build_detected = true;
	}
	break;
	}
	}
	}
	}
	}
	}
	protected function extractBuild($item)
	{
	$assembly_name = $item["placement_annot"]["seq_id_traits_by_assembly"][0]["assembly_name"];
	$assembly_name = explode(".", $assembly_name)[0];
	return intval(substr($assembly_name, -2));
	}
	protected function assignSnp($rsid, $alleles, $chrom)
	{
	// only assign SNP if positions match (i.e., same build)
	foreach ($alleles as $allele) {
	$allele_pos = $allele["allele"]["spdi"]["position"];
	// ref SNP positions seem to be 0-based...
	// print_r($this->get($rsid)["pos"] - 1);
	// echo "\n";
	// print_r($allele_pos);
	if ($allele_pos == $this->get($rsid)["pos"] - 1) {
	$this->setValue($rsid, "chrom", $chrom);
	return true;
	}
	}
	return false;
	}
	public function get($rsid)
	{
	return $this->_snps[$rsid] ?? null;
	}
	public function setValue($rsid, $key, $value)
	{
	echo "Setting {$rsid} {$key} to {$value}\n";
	$this->_snps[$rsid][$key] = $value;
	}
	private function lookupRefsnpSnapshot($rsid, $restClient)

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Summaries of links found in the content:

---

Step 2: ⌨️ Coding

• Modify src/Snps/SNPs.php ✓ d9c9b1b Edit

Modify src/Snps/SNPs.php with contents:
• Update the namespace declaration to match PHP 8.3 standards, ensuring it is at the top of the file following any opening `• Replace the Python-specific libraries and functionalities with their PHP equivalents or alternatives. For instance, use MathPHP for numerical operations instead of numpy, and create or find a suitable library for data manipulation similar to pandas. If a direct equivalent is not available, consider implementing the necessary functionality within the project.
• Convert Python class definitions, methods, and properties into PHP, ensuring to type all properties and method return types according to PHP 8.3 features. This includes using typed properties, arrow functions, and the nullsafe operator where applicable.
• Adapt file I/O operations from Python to PHP, utilizing PHP's built-in functions and classes for reading from and writing to files. This may involve modifying the `Reader` and `Writer` classes in the `src/Snps/IO` directory to ensure compatibility with the updated `SNPs.php` file.
• Implement any missing functionalities that are present in the Python version but not in the PHP version, such as specific SNP analysis methods or data manipulation operations. This may require creating new methods within the `SNPs.php` class or adding new helper classes/functions in the `src/Snps` directory.
• Ensure all modifications and new implementations are thoroughly documented, following PHPDoc standards for documenting classes, properties, and methods. This is crucial for maintainability and understanding of the codebase.
• After making the necessary changes, perform extensive testing to ensure the PHP version matches the functionality of the Python version. This includes unit tests for individual methods and integration tests for the overall SNP analysis functionality.

--- 
+++ 
@@ -1,5 +1,6 @@
 pushHandler(new StreamHandler('php://stderr', Logger::DEBUG));
+
+class SNPs implements Countable, Iterator
 
 class SNPs implements Countable, Iterator
 {
-
     private array $_source = [];
     private array $_snps = [];
     private int $_build = 0;
@@ -56,14 +38,13 @@
     private ?string $_cluster = null;
     private int $_position = 0;
     private array $_keys = [];
-    private array $_duplicate;
-    private array $_discrepant_XY;
-    private array $_heterozygous_MT;
-    private $_chip;
-    private $_chip_version;
-    private $_cluster;
-
-
+    private array $_duplicate = [];
+    private array $_discrepant_XY = [];
+    private array $_heterozygous_MT = [];
+
+
+    /**
+    
     /**
      * SNPs constructor.
      *

• Running GitHub Actions for src/Snps/SNPs.php ✓ Edit

Check src/Snps/SNPs.php with contents:

Ran GitHub Actions for d9c9b1b0ca2ec3cfb6642ab3a738034cb1ca53b5:

---

Step 3: 🔁 Code Review

I have finished reviewing the code for completeness. I did not find errors for sweep/update_snps_2e6a7.

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