From 4d22a34453f023a3e3c499ae46dcce17876d05fe Mon Sep 17 00:00:00 2001
From: mgcam <mg8@sanger.ac.uk>
Date: Thu, 26 Aug 2021 11:30:53 +0100
Subject: [PATCH] Drop redundant tag_index column. (#780)

Drop redundant tag_index column from the tag_metrics database
table. The results of the tag_metrics QC check are always per
lane. Only two distinct values in this culumn - NULL and -1,
the latter from pre-composition times.
---
 Changes                                      |  4 ++++
 lib/npg_qc/Schema/Result/TagMetrics.pm       | 11 ++---------
 npg_qc_viewer/t/80-app-run.t                 |  1 -
 scripts/upgrade_schema/upgrade_schema-69.9.0 |  5 +++++
 4 files changed, 11 insertions(+), 10 deletions(-)

diff --git a/Changes b/Changes
index c3f01beff..f61864599 100644
--- a/Changes
+++ b/Changes
@@ -7,6 +7,10 @@ release 69.9.0
    more data than we envisaged when these tables were set up.
  - Update pulldown_metrics autoqc check to use the up-to-date Picard
    metrics via GATK, use CRAM files instead of BAM files as input.  
+ - Drop redundant tag_index column from the tag_metrics QC database
+   table. The results of this QC check are always per lane. Only two
+   distinct values in this culumn - NULL and -1, the latter from pre-
+   composition times.
 
 release 69.8.1
  - bug fix npg_substitution_metrics.pl to not bail on single read data
diff --git a/lib/npg_qc/Schema/Result/TagMetrics.pm b/lib/npg_qc/Schema/Result/TagMetrics.pm
index f870e91c0..7864ebc8f 100644
--- a/lib/npg_qc/Schema/Result/TagMetrics.pm
+++ b/lib/npg_qc/Schema/Result/TagMetrics.pm
@@ -183,11 +183,6 @@ A foreign key referencing the id_seq_composition column of the seq_composition t
   data_type: 'text'
   is_nullable: 1
 
-=head2 tag_index
-
-  data_type: 'bigint'
-  is_nullable: 1
-
 =head2 tag_hops_percent
 
   data_type: 'float'
@@ -259,8 +254,6 @@ __PACKAGE__->add_columns(
   { data_type => 'text', is_nullable => 1 },
   'info',
   { data_type => 'text', is_nullable => 1 },
-  'tag_index',
-  { data_type => 'bigint', is_nullable => 1 },
   'tag_hops_percent',
   { data_type => 'float', extra => { unsigned => 1 }, is_nullable => 1 },
   'tag_hops_power',
@@ -330,8 +323,8 @@ __PACKAGE__->belongs_to(
 with 'npg_qc::Schema::Composition', 'npg_qc::Schema::Flators', 'npg_qc::autoqc::role::result', 'npg_qc::autoqc::role::tag_metrics';
 
 
-# Created by DBIx::Class::Schema::Loader v0.07048 @ 2018-04-10 14:09:37
-# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:01BT+8rbCPfUeB3ItyFNjQ
+# Created by DBIx::Class::Schema::Loader v0.07049 @ 2021-08-19 13:25:57
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:X85s6Sx84dZtx0r2CpnPQA
 
 our $VERSION = '0';
 
diff --git a/npg_qc_viewer/t/80-app-run.t b/npg_qc_viewer/t/80-app-run.t
index 4dbd35e11..bc7576e15 100644
--- a/npg_qc_viewer/t/80-app-run.t
+++ b/npg_qc_viewer/t/80-app-run.t
@@ -377,7 +377,6 @@ subtest 'Tag metrics as first check in summary table' =>  sub {
       id_run             => 4025,
       position           => $i,
       id_seq_composition => $fkid,
-      tag_index          => -1,
       path=>'some path',
       metrics_file=>'some other path',
       barcode_tag_name=>'BC',
diff --git a/scripts/upgrade_schema/upgrade_schema-69.9.0 b/scripts/upgrade_schema/upgrade_schema-69.9.0
index 3f4652282..fdb472ea6 100644
--- a/scripts/upgrade_schema/upgrade_schema-69.9.0
+++ b/scripts/upgrade_schema/upgrade_schema-69.9.0
@@ -14,3 +14,8 @@ ALTER TABLE `qx_yield` \
   MODIFY `yield2_q30` BIGINT UNSIGNED DEFAULT NULL, \
   MODIFY `yield1_q40` BIGINT UNSIGNED DEFAULT NULL, \
   MODIFY `yield2_q40` BIGINT UNSIGNED DEFAULT NULL;
+
+
+-- Tag metrics results are per lane, tag_index column is not needed
+
+ALTER TABLE `tag_metrics` DROP COLUMN `tag_index`;