Qc check rnaseqc

Changes

@@ -1,5 +1,15 @@
 LIST OF CHANGES FOR NPG-QC PACKAGE
 
+ - remove attribute qc_report_dir from check object: the output directory
+   is created by default using the sample's filename root
+ - upgrade_schema-60.x to create rna_seqc table has been included.
+ - npg_qc::autoqc::qc_store - load rna_seqc results into npg_qc db:
+   requires rna_seqc table exists in database.
+ - updated data/schema.txt including definition for rna_seqc table.
+ - SeQC:
+   - added template for rna_seqc check with selected metrics shown
+     in summary
+   - include a link to original RNA-SeQC report in check's template
  - translation from a database composition representation to the
      npg_tracking::glossary::composition type object
  - db query for compisition-based tables should include a condition

MANIFEST

@@ -264,6 +264,7 @@ lib/npg_qc/Schema/Result/QXYield.pm
 lib/npg_qc/Schema/Result/RecipeFile.pm
 lib/npg_qc/Schema/Result/RefMatch.pm
 lib/npg_qc/Schema/Result/RefSnpInfo.pm
+lib/npg_qc/Schema/Result/RnaSeqc.pm
 lib/npg_qc/Schema/Result/RunAndPair.pm
 lib/npg_qc/Schema/Result/RunConfig.pm
 lib/npg_qc/Schema/Result/RunGraph.pm

data/schema.txt

@@ -1,8 +1,8 @@
 -- MySQL dump 10.13  Distrib 5.5.41, for debian-linux-gnu (x86_64)
 --
--- Host: npgtest-db    Database: npgtest_mg8qc
+-- Host: npgtest-db    Database: npgtest_rb11
 -- ------------------------------------------------------
--- Server version	5.5.31-log
+-- Server version	5.7.13-log
 
 /*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */;
 /*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */;
@@ -1130,6 +1130,40 @@ CREATE TABLE `ref_snp_info` (
 ) ENGINE=InnoDB DEFAULT CHARSET=utf8;
 /*!40101 SET character_set_client = @saved_cs_client */;
 
+--
+-- Table structure for table `rna_seqc`
+--
+
+DROP TABLE IF EXISTS `rna_seqc`;
+/*!40101 SET @saved_cs_client     = @@character_set_client */;
+/*!40101 SET character_set_client = utf8 */;
+CREATE TABLE `rna_seqc` (
+  `id_rna_seqc` bigint(20) unsigned NOT NULL AUTO_INCREMENT COMMENT 'Auto-generated primary key',
+  `id_seq_composition` bigint(20) unsigned NOT NULL COMMENT 'A foreign key referencing the id_seq_composition column of the seq_composition table',
+  `info` text,
+  `rrna` float unsigned DEFAULT NULL,
+  `rrna_rate` float unsigned DEFAULT NULL,
+  `exonic_rate` float unsigned DEFAULT NULL,
+  `expression_profiling_efficiency` float unsigned DEFAULT NULL,
+  `genes_detected` float unsigned DEFAULT NULL,
+  `end_1_sense` float unsigned DEFAULT NULL,
+  `end_1_antisense` float unsigned DEFAULT NULL,
+  `end_2_sense` float unsigned DEFAULT NULL,
+  `end_2_antisense` float unsigned DEFAULT NULL,
+  `end_1_pct_sense` float unsigned DEFAULT NULL,
+  `end_2_pct_sense` float unsigned DEFAULT NULL,
+  `mean_per_base_cov` float unsigned DEFAULT NULL,
+  `mean_cv` float unsigned DEFAULT NULL,
+  `end_5_norm` float unsigned DEFAULT NULL,
+  `end_3_norm` float unsigned DEFAULT NULL,
+  `other_metrics` text,
+  PRIMARY KEY (`id_rna_seqc`),
+  UNIQUE KEY `rna_seqc_id_compos_unq` (`id_seq_composition`),
+  KEY `rna_seqc_compos` (`id_seq_composition`),
+  CONSTRAINT `rna_seqc_compos` FOREIGN KEY (`id_seq_composition`) REFERENCES `seq_composition` (`id_seq_composition`) ON DELETE NO ACTION ON UPDATE NO ACTION
+) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+/*!40101 SET character_set_client = @saved_cs_client */;
+
 --
 -- Table structure for table `run_and_pair`
 --
@@ -1697,4 +1731,4 @@ CREATE TABLE `verify_bam_id` (
 /*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */;
 /*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */;
 
--- Dump completed on 2016-02-25 13:46:17
+-- Dump completed on 2016-12-06 11:53:49