static function performLikelihoodRateFilter($con, $previousTable, $currentTable, $args)
{
if ($args == null || count($args) == 0) {
return;
} else {
if (count($args) != 2) {
REDLog::writeErrLog("Args for Likelihood Rate Test Filter are incomplete, please have a check");
}
}
$dnaVcfTable = $args[0];
$threshold = (double) $args[1];
TableCreator::createFilterTable($con, $previousTable, $currentTable);
REDLog::writeInfoLog("Start performing Likelihood Rate Test Filter");
$sqlClause1 = "select {$previousTable}.chrom,{$previousTable}.pos,{$previousTable}.AD,\n{$dnaVcfTable}.qual from {$previousTable},{$dnaVcfTable} where {$previousTable}.chrom=\n{$dnaVcfTable}.chrom and {$previousTable}.pos={$dnaVcfTable}.pos";
$rs = DatabaseManager::query1($con, $sqlClause1);
$i = 0;
while ($row = mysqli_fetch_array($rs)) {
$chr = (string) $row[0];
$pos = (int) $row[1];
$ad = (string) $row[2];
$qual = (double) $row[3];
$pb = new SiteBean();
$pb->SiteBean1($chr, $pos);
$pb->setAd($ad);
$pb->setQual($qual);
$siteBeans[$i] = $pb;
$i++;
}
DatabaseManager::setAutoCommit($con, false);
$count = 0;
for ($j = 0; $j < $i; $j++) {
$str = $siteBeans[$j]->getAd();
$section = explode("/", $str);
$ref = (int) $section[0];
$alt = (int) $section[1];
if ($ref + $alt > 0) {
$f_ml = 1.0 * $ref / ($ref + $alt);
$y = pow($f_ml, $ref) * pow(1 - $f_ml, $alt);
$y = log($y) / log(10.0);
$judge = $y + $siteBeans[$j]->getQual() / 10.0;
if ($judge >= $threshold) {
$siteChr = $siteBeans[$j]->getChr();
$sitePos = $siteBeans[$j]->getPos();
$sqlClause2 = "insert into {$currentTable} select * from {$previousTable} where chrom='" . $siteChr . "' and pos=" . $sitePos;
DatabaseManager::insertClause($con, $sqlClause2);
if (++$count % 10000 == 0) {
DatabaseManager::commit($con);
}
}
}
}
DatabaseManager::commit($con);
DatabaseManager::setAutoCommit($con, true);
REDLog::writeInfoLog("End performing Likelihood Rate Test Filter");
}
static function performQualityControlFilter($con, $previousTable, $currentTable, $args)
{
$COMMIT_COUNTS_PER_ONCE = 10000;
if ($args == null || count($args) == 0) {
return;
} elseif (count($args) != 2) {
REDLog::writeErrLog("Args for Quality Control Filter are incomplete, please have a check");
}
$quality = (double) $args[0];
$depth = (int) $args[1];
TableCreator::createFilterTable($con, $previousTable, $currentTable);
REDLog::writeInfoLog("Start performing Quality Control Filter");
try {
$count = 0;
$str = array("CHROM", "POS", "AD");
$rs = DatabaseManager::query2($con, $previousTable, $str, null, null);
$i = 0;
while ($row = mysqli_fetch_array($rs)) {
if ($row[2] != null) {
$siteBean = new SiteBean();
$siteBean->SiteBean1($row[0], $row[1]);
$siteBean->setAd($row[2]);
$siteBeans[$i] = $siteBean;
$i = $i + 1;
}
}
DatabaseManager::setAutoCommit($con, false);
for ($j = 0; $j < $i; $j++) {
$str = $siteBeans[$j]->getAd();
$section = explode("/", $str);
$ref_n = (int) $section[0];
$alt_n = (int) $section[1];
$pos = $siteBeans[$j]->getPos();
$chr = $siteBeans[$j]->getChr();
if ($ref_n + $alt_n >= $depth) {
$sqlClause = "insert into " . $currentTable . " (select * from " . $previousTable . " where filter='PASS' and pos={$pos} and qual>=" . $quality . " and chrom='" . $chr . "')";
$v = mysqli_query($con, $sqlClause);
if (++$count % $COMMIT_COUNTS_PER_ONCE == 0) {
DatabaseManager::commit($con);
}
}
}
DatabaseManager::commit($con);
DatabaseManager::setAutoCommit($con, true);
if (!$v) {
throw new Exception("Error execute sql clause in QualityControlFilter:performFilter()");
}
} catch (Exception $e) {
REDLog::writeErrLog($e->getMessage());
}
REDLog::writeInfoLog("End performing Quality Control Filter");
}
