initial commit of script to analyse crispr damage from a scf trace file
Initial commit of module to extract variant sequence from SCF file
start working with SCF files with heterozygous sequences, updated pod
bugfix, regex should be A-Z not A-z, also uppercase base we are looking to replace just before a insertion, there is a small change this base could be a mismatch and would thus be represented by a lowercase letter
uppercase the variant sequence
Update ENV variables to point away from temporary values, added pod
add tests for HTGT::QC::Util::SCFVariationSeq module
Add tests for HTGT::QC::Util::DrawPileupAlignment
Added POD to tests, renamed test_data files for scf variation tests
turn off log output
moved common constants into new HTGT::QC::Constants module
remove unused module
add black box tests for HTGT::QC::Util::CrisprDamageVEP module
make CrisprDamageVEP module use values from Constants module
remove unused module use
can pass in custom reference seq if needed
use Bio::SeqIO module
initial commit of script to analyse scf files from harwell
do not need LIMS2::Model in script
Initial commit of module that will merge multiple variants in a VCF file into one and create a new VCF file based on this merged variant