Calculate normalised read depth ratios from normal bam; af from obs/ex read support

Read depth

• Major update to calculate read depth ratios on the fly when 'normal' bam provided
• Will use the number of reads in both bams to normalise for different sequencing depths between samples

Allele frequency

• Now use the observed / expected values to adjust allele frequency for tumour purity

Get regions

• Now just take regions surrounding bps (+/- 500 currently - should adj to scale for fragment length)
• This greatly increases speed as:
  • No longer need to search whole file for mates
  • Now just merge reads surrounding bps (rather than all contained within bps)

v0.6.1 - Fix pysam index bug

Fix indexing bug

v0.5.2 - Improve guesswork

Improve guesswork by using softclipped reads

v0.5 - minor improvements and bug fixes

version 0.5 - Revert to orignals bps if not able to hone; panads in c…

v0.4 - common class for all types & read config for batch process

version 0.4; Shared class for all events; read config for batch proce…

v0.3 - calculate for fragments; filter opposing for supporting

version 0.3 - calculate for fragments (not reads); fiter opposing for…

v0.2 - shared functions into modules

version 0.2 - move shared functions into modules

v0.1 - first release

version 0.1 - first version - works for deletions