2017/5/26 - Telomerecat v3.1.2 - jhrf

- Added a check in bam2telbam rule that ensures the read.seq is loaded into
  the read and does not return None. This was causing a hang in PCAWG samples 
- Tidied up the code surrounding mismatching loci following code review.
  Process should be easier to follow now
- Minor bug fixes and restructing in telbam2length
- Changed the requirements such that a fixed version of pysam is required
  this version is proven stable and more recent versions have caused crashes

2017/1/24 - Telomerecat v3.1.1 - jhrf

- Removed debug print message from telbam2length

2017/1/17 - Telomerecat v3.1 - jhrf

- Added the ability to specify a read trim via the command line
- Made the telbam2length estimation protocol more responsive to differing
  read lengths (i.e removed magic numbers)
- Fixed command line parameterisation bugs in csv2length and telbam2length