static function performDNARNAFilter($con, $previousTable, $currentTable, $args)
{
if ($args == null || count($args) == 0) {
return;
} else {
if (count($args) != 2) {
REDLog::writeErrLog("Args for DNA-RNA Filter are incomplete, please have a check");
}
}
TableCreator::createFilterTable($con, $previousTable, $currentTable);
REDLog::writeInfoLog("Start performing DNA-RNA Filter");
$dnaVcfTable = $args[0];
$editingType = $args[1];
$negativeType = REDTools::getNegativeStrandEditingType($editingType);
try {
$num1 = substr($editingType, 0, 1);
$num2 = substr($negativeType, 0, 1);
$sqlClause = "insert into {$currentTable} select * from {$previousTable} where exists (select chrom\nfrom {$dnaVcfTable} where ({$dnaVcfTable}.chrom={$previousTable}.chrom and {$dnaVcfTable}.pos={$previousTable}.pos and (\n{$dnaVcfTable}.ref='{$num1}' or {$dnaVcfTable}.ref='{$num2}')))";
$v = mysqli_query($con, $sqlClause);
if (!$v) {
throw new Exception("Error execute sql clause in performDNARNAFilter");
}
} catch (Exception $e) {
REDLog::writeErrLog($e->getMessage());
}
REDLog::writeInfoLog("End performing DNA-RNA Filter");
}
static function performEditingTypeFilter($con, $previousTable, $currentTable, $args)
{
REDLog::writeInfoLog('Star executing Editing Type Filter');
TableCreator::createFilterTable($con, $previousTable, $currentTable);
$refAlt = $args;
$refAlt2 = REDTools::getNegativeStrandEditingType($refAlt);
$sql11 = substr($refAlt, 0, 1);
$sql12 = substr($refAlt, 1);
$sql21 = substr($refAlt2, 0, 1);
$sql22 = substr($refAlt2, 1);
$sql1 = "insert into " . $currentTable . " select * from " . $previousTable . " WHERE REF='{$sql11}' AND ALT='{$sql12}' AND GT!='0/0'";
$v = DatabaseManager::insertClause($con, $sql1);
if (!$v) {
REDLog::writeErrLog('There is a syntax error for SQL clause:' . $sql1);
}
$sql2 = "insert into " . $currentTable . " select * from " . $previousTable . " WHERE REF='{$sql21}' AND ALT='{$sql22}' AND GT!='0/0'";
$v = DatabaseManager::insertClause($con, $sql2);
if (!$v) {
REDLog::writeErrLog('There is a syntax error for SQL clause:' . $sql2);
}
REDLog::writeInfoLog('End executing Editing Type Filter');
}
<?php
include '../REDTools/REDTools.php';
echo REDTools::getNegativeStrandEditingType('TC');
