README update

MANIFEST

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 lib/npg_qc/utils/genotype_calling.pm
 MANIFEST
 README
+README.md
+README_QC.md
 scripts/npgqc_dbix_schema_loader.pl
 t/00-critic.t
 t/00-distribution.t

README

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+README.md

README.md

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+# QC Checks and Metrics for Illumina Next Generation Sequencing Data
+
+## Listing of Directories
+
+### lib
+
+ - npg_qc::Schema namespace - DBIx ORM
+ - npg_qc::illumina namespace - db loaders for Illumina QC metrics
+ - npg_qc::autoqc namespace - WSI core sequencing pipeline in-house
+     QC checks and storage of QC metrics
+ - npg_qc::mqc - evaluation an dreporting of QC metrics
+
+### bin
+
+Perl scripts which are deployed to the production environment
+
+### scripts
+
+Supplimentary scripts, not deployed
+
+### t
+
+Tests, test data, supplimentary scripts and modules for testing
+
+### npg_qc_viewer
+
+Source code for the web server that displays the QC metrics
+
+### docs
+
+Documentation, useful code snippets
+
+## NPG QC database
+
+### Legacy Data
+
+QC metrics and evaluation outcomes for all production Illumina sequensing runs
+are stored in a relational database. This database has four legacy tables,
+`recipe_file`, `run_and_pair`, `run_info`, `run_recipe`, for which we do not
+generate ORM classes. No code is using these tables. The data is kept for
+auditing perposes. The size of these tables is small in comparison with the size
+of the rest of the tables. The overhead of moving these old tables to a different
+storage is not justified.
+
+