echo "Ref Matches: " . $identityarray[0] . "/" . $identityarray[1] . "<br>";
displayalignment($alignarray['r_align_string'], $alignarray['q_align_string'], $alignarray['r_start'], $alignarray['q_start'], $alignarray['alignstrand']);
} elseif ($align2_result->num_rows >= 1) {
foreach ($align2_result as $row) {
while ($property = mysqli_fetch_field($align2_result)) {
//echo "<p>" . $property->name . " : " . $row[$property->name] . "</p>";
$align2array[$property->name] = $row[$property->name];
}
}
$samtomaf = samtomaf($align2array['qname'], $align2array['flag'], $align2array['rname'], $align2array['mapq'], $align2array['cigar'], $align2array['rnext'], $align2array['pnext'], $align2array['tlen'], $align2array['seq'], $align2array['qual'], $align2array['n_m'], $align2array['m_d'], $align2array['pos']);
$identityarray = alignsim($samtomaf[0], $samtomaf[1]);
echo "Read Name: " . $align2array['basename'] . " Reference Name: " . $align2array['refname'] . "<br>";
echo "% identity: " . round($identityarray[0] * 100 / strlen($samtomaf[0]), 2) . "<br>";
echo "Query Matches: " . $identityarray[0] . "/" . $identityarray[2] . "<br>";
echo "Ref Matches: " . $identityarray[0] . "/" . $identityarray[1] . "<br>";
displayalignment($samtomaf[0], $samtomaf[1], $samtomaf[2], $samtomaf[3], $alignarray['align2strand']);
} else {
echo "No Alignment<br>";
}
?>
</div>
</div>
</div>
</div>
<?php
echo "</div>";
//var_dump($resultsarray);
echo "</div>";
echo "</div>";
}
$align = "SELECT * FROM last_align_maf_basecalled_complement inner join reference_seq_info using (refid) inner join config_general using (basename_id) where config_general.basename = '" . $_POST['readname'] . "';";
$align_result = $mindb_connection->query($align);
$alignarray;
if ($align_result->num_rows >= 1) {
foreach ($align_result as $row) {
while ($property = mysqli_fetch_field($align_result)) {
//echo "<p>" . $property->name . " : " . $row[$property->name] . "</p>";
$alignarray[$property->name] = $row[$property->name];
}
}
$identityarray = alignsim($alignarray['r_align_string'], $alignarray['q_align_string']);
echo "Read Name: " . $alignarray['basename'] . " Reference Name: " . $alignarray['refname'] . "<br>";
echo "% identity: " . round($identityarray[0] * 100 / strlen($alignarray['r_align_string']), 2) . "<br>";
echo "Query Matches: " . $identityarray[0] . "/" . $identityarray[2] . "<br>";
echo "Ref Matches: " . $identityarray[0] . "/" . $identityarray[1] . "<br>";
displayalignment($alignarray['r_align_string'], $alignarray['q_align_string'], $alignarray['r_start'], $alignarray['q_start'], $alignarray['alignstrand']);
} else {
echo "No Alignment<br>";
}
?>
</div>
</div>
</div>
</div>
<?php
echo "</div>";
//var_dump($resultsarray);
echo "</div>";
echo "</div>";
}
