sql/schema_mysql.sql
Split cas9 table into cas9 and cas9_prep.
Changes to SQL schema.
sql/schema_mysql.sql
Added column guideRNA_prep_id to tables guideRNA_prep and injection_pool.
Moved column guideRNA_type from injection to guideRNA_prep.
Moved columns guideRNA_concentration from injection to injection_pool.
New File: scripts/add_targets_to_db_from_file.pl
For adding CRISPR target regions to an SQL database.
Corrected Documentation of _fetch methods.
Changes to TargetAdaptor fetch methods

lib/Crispr/DB/TargetAdaptor.pm
Added _fetch method and changed other fetch methods to call _fetch.
Changes to Cas9 object

lib/Crispr/Cas9.pm
Added db_id, plasmid_name and notes methods
attribute type now has a list of accepted values.

t/cas9.t
Changes to test new attributes

New File: lib/Crispr/DB/Cas9Adaptor.pm
Adaptor for Cas9 to reflect new Cas9 table

New File: t/cas9_adaptor.t
Test file for Cas9Adaptor
lib/Crispr/DB/Cas9PrepAdaptor.pm
Added cas9_adaptor attribute
Added checking that Cas9 exists in the db.
Changed SQL in store_cas9_preps, fetch_without_db_id, fetch_all_by_type
and _fetch
Changed _make_new_cas9_prep_from_db to reflect changes

t/cas9_prep_adaptor.t
Changes to reflect changes to cas9 and cas9_prep
lib/Crispr/DB/Cas9Prep.pm
Corrected Documentation
t/base_adaptor.t
Made changes to reflect changes to cas9 table in schema
lib/Crispr/DB/InjectionPool.pm
Changed guideRNAs from crRNA objects to GuideRNAPrep ones.
Removed guideRNA_conc and guideRNA_type attributes (Now handled by guideRNA objects)

t/injection_pool.t
Changes to reflect chanes to InjectionPool object

lib/Crispr/DB/InjectionPoolAdaptor.pm
Added guideRNA_prep_adaptor attribute
Corrected the SQL statements for adding to injection and injection_pool tables
Changed SQL in _fetch

t/injection_pool_adaptor.t
Changes to reflect changes to Cas9 and InjectionPool objects
lib/Crispr/DB/GuideRNAPrep.pm
Added db_id, type and well attributes
lib/Crispr/Plate.pm
Added some new plate types to plate_category attribute
sql/schema_mysql.sql
Added some new plate types to plate_category column
Made cas9 type and plasmid_name UNIQUE
table injection pool - made primary key injection_id and guideRNA_prep_id
GuideRNAPrepAdaptor object.

New File: lib/Crispr/DB/GuideRNAPrepAdaptor.pm
Adaptor for storing and fetching GuideRNAPreps to/from the database.

New File: t/guideRNA_prep_adaptor.t
Test file.
lib/Crispr/DB/DBConnection.pm
Added adaptor types cas9 and guideRNA_prep to get_adaptor
lib/Crispr/DB/crRNAAdaptor.pm
Corrected _make_new_crRNA_from_db
t/target_adaptor.t
Changed Target object to MockObject
sql/schema_mysql.sql
Changed mismatches in table off_target_info from VARCHAR(60) to TINYINT
Changes to crRNAAdaptor object

lib/Crispr/DB/crRNAAdaptor.pm
Changed store/store_crRNA/store_crRNAs so that only crRNA table is populated.
Use other methods provided to add coding scores, off-targets,
restriction enzymes, construction oligos, expression constructs and primers.
Changed store_off_target_scores to store_off_target_info and altered it to
use the new OffTargetInfo object

t/crRNA_adaptor.t
Changed test to check storing of off-target-info in db
Changes to Crispr design object
lib/Crispr.pm
Fixed bug in create_crRNA_from_crRNA_name.

t/crispr.t
Added comment about the mock off-target positions