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
Crispr - altered create_crRNA_from_crRNA_name.

Changed create_crRNA_from_crRNA_name to only add sequence to new crRNA
object if it's defined.
Added comment to method create_crRNA_from_crRNA_name.
lib/Crispr/OffTargetInfo.pm - added end of line semi-colon

scripts/crispr_pairs_for_deletions.pl - Corrected typo. missing sigil.
Corrected typos. Missing sigils.
scripts/crispr_pairs_for_deletions.pl
new subroutine: fetch_gene. refactored code to make sure script supports RNASEQ genes
scripts/design_pcr_primers_for_illumina_screening.pl
Changed external product size range and added more exclusion around target for
external pair to give more space for internal design.
Now prints out external product size as well as internal.