Update design data to csv script to revcom the gibson oligos as needed
clarify invertion of sequence, not revcomp
add genomic specificity check to gibson oligo filtering
change log level of exonerate messages
initial commit of document about gibson
use Bio::SeqIO module, note down fix that needs to be made to code
update filter gibson oligos tests to deal with exonerate checks
initial commit of design target finder for just human gibson designs
moved gibson specific criteria to new script, added output of failed targets
added first attempt at loose criteria for human gibson targets
add back exon closeness check with better method of checking, stops too many false positives
remove loose flag, not useful at present, added better logging and recording of reason why a given gene does not have any valid targets
initial commit of BWA util module
add code to parse sam files into sorted bam files
add code to parse bed files to bed files and grab sequence for hits
add code to grab original oligo seqs and to calculate hamming distance
update gibson docs
fix misleading comment about inverting a ensembl slice
Refactor running of bwa related commands into different subroutines.
Add option for a more specific check of the 3' end of the oligo for
alignments ( code not complete ).
Default to just counting the number of hits we get for each oligo.
Add flags to control deletion of intermediate files.
If we are not doing the three prime check them we can parse the sam file
for hit information, saves time as we can skip mulitple steps.
Code tidy up and pod updating.