allow bad rna samples in somatic an_rna step

imgag · Apr 4, 2023 · b94b8f1 · b94b8f1
1 parent 5772567
commit b94b8f1
Showing 1 changed file with 3 additions and 4 deletions.
diff --git a/src/Pipelines/somatic_dna.php b/src/Pipelines/somatic_dna.php
@@ -945,13 +945,12 @@ function($str) { return explode("\t", $str); },
 		//get related RNA samples from NGSD
 		if (count($res) >= 1)
 		{
-			$res = $db->executeQuery("SELECT * FROM sample_relations WHERE relation='same sample' AND (sample1_id=:sid OR sample2_id=:sid)", array("sid" => $sample_id));
-			foreach($res as $row)
+			$relations = $db->executeQuery("SELECT * FROM sample_relations WHERE relation='same sample' AND (sample1_id=:sid OR sample2_id=:sid)", array("sid" => $sample_id));
+			foreach($relations as $row)
 			{
 				$sample_id_annotation = $row['sample1_id'] != $sample_id ? $row['sample1_id'] : $row['sample2_id'];
 
-				$res = $db->executeQuery("SELECT ps.sample_id, ps.process_id, ps.processing_system_id, ps.quality, sys.id, sys.type, CONCAT(s.name, '_', LPAD(ps.process_id, 2, '0')) as psample FROM processed_sample as ps, processing_system as sys, sample as s WHERE ps.sample_id=:sid AND sys.type='RNA' AND ps.processing_system_id=sys.id AND ps.sample_id=s.id AND (NOT ps.quality='bad')", array("sid" => $sample_id_annotation));
-
+				$res = $db->executeQuery("SELECT ps.sample_id, ps.process_id, ps.processing_system_id, ps.quality, sys.id, sys.type, CONCAT(s.name, '_', LPAD(ps.process_id, 2, '0')) as psample FROM processed_sample as ps, processing_system as sys, sample as s WHERE ps.sample_id=:sid AND sys.type='RNA' AND ps.processing_system_id=sys.id AND ps.sample_id=s.id", array("sid" => $sample_id_annotation));
 				$rna_ids = array_column($res, 'psample');
 				foreach($rna_ids as $rna_id)
 				{