Commit 68d08772 authored by Maxime Manno's avatar Maxime Manno 🍜
Browse files

Update Smarty template for N90 and logest reads #16

parent af0d1599
......@@ -169,6 +169,8 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{foreach from=$rawdata_headers key=k item=head}
{assign var="headQ7" value=$head|cat:"_Q7"}
{assign var="headQ9" value=$head|cat:"_Q9"}
{assign var="count_longread" value=1}
{assign var="corresp_num" value=['1' => 'First', '2' => 'Second', '3' => 'Third', '4' => 'Fourth', '5' => 'Fifth']}
<tr>
{if ($head == 'mean_read_quality')}
<td><label>{$head|replace:'_':' '}</label></td>
......@@ -185,6 +187,12 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<td>{($rawdata.$head)|number_format:0:',':' '}</td>
<td>{($Q7.$headQ7)|number_format:0:',':' '} ({($Q7.$headQ7 / $rawdata.total_bases*100)|number_format:2:',':' '}%)</td>
<td>{($Q9.$headQ9)|number_format:0:',':' '} ({($Q9.$headQ9 / $rawdata.total_bases*100)|number_format:2:',':' '}%)</td>
{elseif ($head|strstr:"longread")}
{assign var="corresp" value=$head|replace:'longread':''}
<td><label>{$corresp_num[$corresp]} longest read</label></td>
<td>{($rawdata.$head)|number_format:0:',':' '}</td>
<td>{($Q7.$headQ7)|number_format:0:',':' '}</td>
<td>{($Q9.$headQ9)|number_format:0:',':' '}</td>
{else}
<td><label>{$head|replace:'_':' '}</label></td>
<td>{($rawdata.$head)|number_format:0:',':' '}</td>
......@@ -374,6 +382,9 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
</li>
<li><strong>N50 read length</strong> :
50% of all bases come from reads longer than this value.
</li>
<li><strong>N90 read length</strong> :
90% of all bases come from reads longer than this value.
</li>
<li><strong>Mean read quality</strong> :
The mean quality (qscore ONT) for this Flow Cell.
......
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