b/lib/Crispr.pm
Changed method bwa_align to avoid reliance on bwa being installed at specific place.
Now it justs needs to be in the user's path.
Changed off_target to parsing sam output directly.
Added code to filter_and_score_off_targets for parsing supplementary alignments
from bam files.
Removed subroutine make_bam_and_bed_files.
Changed score_off_targets_from_bed_output to score_off_targets_from_sam_output.
scripts/find_and_score_crispr_sites.pl
Script to search for and score potentials crispr target sites.
Input is either Ensembl ids (Gene, Transcript, Exon) or genomic region
or a combination of all.
Possible crispr sites can be scored for off-target potential
and coding position.
lib/Crispr.pm
Added _testing method to allow warning messages from bwa to be ignored when
running test files.
Corrected bug in filter_and_score_off_targets to get strand right.

t/crispr.t
Altered attribute and method calling tests.
Changed genome and annotation attributes to test files in t/data directory.
Added tests for methods all_crisprs, targets, filter_crRNAs_from_target_by_strand,
create_crRNA_from_crRNA_name, off_targets_bwa, calculate_all_pc_coding_scores,
calculate_pc_coding_scores, filter_crRNAs_from_target_by_score and remove_target
t/crRNA.t
Added tests for target_summary_plus_crRNA_info & target_info_plus_crRNA_info
methods.
data files for use by test files.