Files for setting up database schema and inserting some base data.

sql/schema_mysql.sql - Schema for a MySQL db
sql/insert_enzymes.sql - SQL statments to insert enzyme info for NEB enzymes
sql/insert_enzyme_ordering_info.sql - SQL statements to insert oredering
info for enzymes
sql/insert_plasmid_backbone.sql - SQL statements to add plasmid information
Removed Multi-line comment that was messing up execution of the SQL.
lib/Crispr/Adaptors/DBAttributes.pm - Moose Role for use by DB Adaptors
Added test file for DBAttributes.pm

t/db_attributes.t - Test File
t/lib/TestDB.pm - Module that creates a test db and destroys it at the end if necessary.
Changes to DBAttributes

lib/Crispr/Adaptors/DBAttributes.pm
Changed fetch_rows_expecting_single_row to simplify the data structure returned.

t/db_attributes.t
Changed it so that it correctly skips tests if the MySQL environment variables are not set.
Changes to Target

lib/Crispr/Target.pm
Removed some unneccessary Documentation

t/target.t
Changed name to target_name to fit with new Target attribute name

t/data/test_data_targets.txt
Changed name to target_name to fit with new Target attribute name
t/lib/TestDB.pm
Added debug attribute to TestDB to allow for debugging
Corrected converting MySQL to SQLite
lib/Crispr/Adaptors/DBAttributes.pm
Changed check_entry_exists_in_db - better error checking

t/db_attributes.t
New Tests - testing check_entry_exists_in_db
TargetAdaptor

New File:
lib/Crispr/Adaptors/TargetAdaptor.pm - Module for TargetAdaptor object.

New File:
t/target_adaptor.t - Test file
Changes to crispr.t - Changed mock genome to be much smaller.
Changed mock crRNA objects to fit with this.
lib/Crispr.pm
Added internal method _fetch_sequence to get sequence for potential off-target
hits from either Ensembl or a genome fasta file.
t/crispr.t
Changed mocking of methods to allow testing of bwa off-target checking and then coding score calculation

t/lib/TestMethods.pm
Changed Documentation
Changes to Targets object

lib/Crispr/Target.pm
Changed name of Target attribute to target_name for less ambiguity

lib/Crispr.pm
Changes to Crispr.pm to reflect change of target name attribute to target_name

t/crispr.t
Changes to reflect changes to Target object

t/target.t
Changes to reflect changes to Target object

lib/Crispr/crRNA.pm
Changes to reflect changes to Target object
lib/Crispr.pm
Added code to create_crRNA_from_crRNA_name to get sequence for crRNA object
Changes to OffTarget scoring

lib/Crispr/OffTarget.pm
Changed OffTarget object. Now each off_target hit is represented by a separate
OffTarget object, which are all held in a new OffTargetInfo object.
OffTarget object now has attributes crRNA_name, chr, start, end, strand, mismatches and annotation
and method position.

lib/Crispr/OffTargetInfo.pm - New File:
New OffTargetInfo object to hold OffTarget objects.
Has private attribute _off_targets and methods add_off_target, all_off_targets,
score, info, off_target_counts, off_target_hits, number_exon_hits, number_intron_hits and
number_nongenic_hits.

t/off_target.t and t/off_target_info.t
Test Files changed to reflect changes to OffTarget objects.

lib/Crispr.pm
Changes to Crispr.pm to reflect changes in OffTarget scoring
Changed name of off_targets_bwa to find_off_targets

t/crispr.t
Changes to reflect changes to OffTarget object

lib/Crispr/crRNA.pm
Changed off_target_hits from OffTarget object to OffTargetInfo object

t/crRNA.t
Changed $mock_off_target_object to reflect changes to OffTarget object
scripts/crispr_pairs_for_deletions.pl
Changed off_target code to fit with new OffTarget objects

scripts/find_and_score_crispr_sites.pl
Changed off_targets_bwa to find_off_targets
.gitignore
Added t/data/zv9_* and t/data/e*annotation.gff
lib/Crispr/crRNA.pm
Changed output of method info to reflect changes to OffTarget scoring

scripts/crispr_pairs_for_deletions.pl
scripts/find_and_score_crispr_sites.pl
Changed header to reflect changes to OffTarget
Changed name to target_name
lib/Crispr/crRNA.pm
Added method base_composition
Added GC content to info method

t/crRNA.t
Added tests for base composition

scripts/crispr_pairs_for_deletions.pl
Changed header to include GC content and notes

scripts/find_and_score_crispr_sites.pl
Changed code for base composition, GC content and pre-PAM base checking
Changed header to include GC content and notes
lib/Crispr.pm - Check slice_adaptor is defined in method _fetch_sequence