v0.017

    Added CrisprAlleleDamage module and util method to get cigar parsed read names
initial commit of crispr damage VEP / VCF module
add code to run vep script
produce vcf file which only looks at target region
Initial commit of module that will convert a pileup file back into a aligned sequence
insert 1 character for insertions, do not try to insert whole sequence, add method to create truncated sequences
Clean up read sequences by swapping dashes for N characters.
Generate alignment strings for the reads so we can show users a simple
alignment diagram.
Do not run vep if we have no variants in the target region.
calculate genome_end coordinates in addition to genome_start, remove empty alignments, no longer add additional truncated alignment sequences
store the pileup_parser as a attribute so we can access all its information
filter out reads that do not overlap target region
write out file with alignment text strings.
bugfix, correctly work out where to put the base after end of string character in pileup.
replace spaces with X characters to better show alignments
must still insert a character in the X region of a read alignment, otherwise alignments will be offset
store number of target region alignments.
send the target chromosome to the pileup parser module.
Change gap open penalty on bwa mem to 2, the default is 6, this should make bwa mem better align reads with large deletions
temp fix for non consecutive bases in pileup file
Add more logging
Bugfix, add the correct pileup read to the second read
Store the last genome position of the pileup
do not need dsign strand attribute
target string for filtering reads expanded by 200 bases to caputure reads that are in target region but do not hit target region.
target string for filtering vcf file padded by 10 bases to each side to get varients close to the target region
specify following then running ensembl vep script:
species
symbol flag to report gene symbol
canonical flag to mark the canonical transcript in output
per_gene flag to only output the most severe consequence per gene
create a deletions hash alongside the insertions hash
Change the way we display insertions in the aligned sequence:
Use multiple characters to represent where a insertion took place, will map back to original base.
Insertion character replaces base before the insertion, previously it was inserted between bases.
add TODO node about filling in missing reference sequence