Commit f0df9644 authored by Claire Kuchly's avatar Claire Kuchly
Browse files

move to BWA mem

parent d28a2bf8
......@@ -58,21 +58,23 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<th rowspan="2" style="vertical-align:Middle"><center><input type="checkbox" id="chk_all_sample"></center></th>
<th rowspan="2" class="string-sort" style="vertical-align:Middle">Samples {if $analyse_results|@count > 1 }({$analyse_results|@count}){/if}</th>
<th colspan="3">Reads</th>
<th colspan="6">Alignment</th>
<th colspan="3">Duplication</th>
<th colspan="5">Alignment</th>
</tr>
<tr>
<th class="numeric-sort" style="vertical-align:Middle"><center>Paired</center></th>
<th class="numeric-sort" style="vertical-align:Middle"><center>Read1</center></th>
<th class="numeric-sort" style="vertical-align:Middle"><center>Read2</center></th>
<th class="numeric-sort" style="vertical-align:Middle"><center>Duplicated</center></th>
<th class="numeric-sort" style="vertical-align:Middle"><center>Read pair duplicates</center></th>
<th class="numeric-sort" style="vertical-align:Middle"><center>Read pair optical duplicates</center></th>
<th class="numeric-sort" style="vertical-align:Middle"><center>Mapped</center></th>
<th class="numeric-sort" style="vertical-align:Middle"><center>Properly paired</center></th>
<th class="numeric-sort" style="vertical-align:Middle"><center>With itself and mate mapped</center></th>
<th class="numeric-sort" style="vertical-align:Middle"><center>Singletons</center></th>
<th class="numeric-sort" style="vertical-align:Middle"><center>Mate mapped on a different chr</center></th>
<th class="numeric-sort" style="vertical-align:Middle"><center>Supplimentary</center></th>
<th class="numeric-sort" style="vertical-align:Middle"><center>Duplicated</center></th>
<th class="numeric-sort" style="vertical-align:Middle"><center>Read pair duplicates</center></th>
<th class="numeric-sort" style="vertical-align:Middle"><center>Read pair optical duplicates</center></th>
</tr>
</thead>
<tbody>
......@@ -109,6 +111,12 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{assign var="mapped" value=" "|explode:$sample_results["default"].mapped}
{assign var="properlypaired" value=" "|explode:$sample_results["default"].properlypaired}
{assign var="singletons" value=" "|explode:$sample_results["default"].singletons}
<td>{$mapped[0]|number_format:0:' ':' '} {$mapped[1]}</td>
<td>{$properlypaired[0]|number_format:0:' ':' '} {$properlypaired[1]}</td>
<td>{$sample_results["default"].matemapped|number_format:0:' ':' '}</td>
<td>{$singletons[0]|number_format:0:' ':' '} {$singletons[1]}</td>
<td>{$sample_results["default"].mapch1|number_format:0:' ':' '}</td>
<td>{$sample_results["default"].supplimentary|number_format:0:' ':' '}</td>
{if !isset($sample_results["default"]["pairOpticalDuplicates"]) }
<td>-</td>
<td>-</td>
......@@ -118,11 +126,6 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<td>{$sample_results["default"].pairDuplicates|number_format:0:' ':' '}</td>
<td>{$sample_results["default"].pairOpticalDuplicates|number_format:0:' ':' '}</td>
{/if}
<td>{$mapped[0]|number_format:0:' ':' '} {$mapped[1]}</td>
<td>{$properlypaired[0]|number_format:0:' ':' '} {$properlypaired[1]}</td>
<td>{$sample_results["default"].matemapped|number_format:0:' ':' '}</td>
<td>{$singletons[0]|number_format:0:' ':' '} {$singletons[1]}</td>
<td>{$sample_results["default"].mapch1|number_format:0:' ':' '}</td>
</tr>
{$i = $i +1}
{/foreach}
......
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