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.
add bwa work dir to constants
Update pod
Switch from exonerate to bwa in filter gibson oligo step
add document with notes about bwa alignments
add NoGetopt trait to attribute
turn off exon flank check by default
renmae okay_hit to risky to make clear its probably not a good hit
do not append to log file, over-write it
do not skip hits with mismatch bases
Merge branch 'devel' into bwa
use default exonerate model, ungapped, instead of affine:local