Merge branch 'master' of https://github.com/andrewjpage/Bio-Tradis
Extra Tradis steps

No testing yet.
Maybe[Str] fix

Problems with undef outfile
Changed default location

Moved default setting to command line pm
Mapping test added

+ other minor fixes
Completed pipeline

with tests. First pass.
Test file changes

minor
Basic parsers added

BAM and fastq parsers added and integrated
Added new features

- new parsers added
- stats file generated (needs more testing)
- quality score filtering when creating plots
- tag direction option
- 0.96 default mapping score
- k & s parameters for reference indexing calculated
- file list as input
Added tag mismatch option

Users may specify how many mismatches are allowed when matching tags
Added tag mismatch option

Users specify # mismatches allowed when matching tags
Compete pipeline v1
Naming convention update
Tidying up
Updated stats

Handles >1 plot file
Added UIS/seq len + totals
Tidying test data
Minor fix

Switched print statement to STDERR
Removed useless hidden file
Stats as CSV
Handle full paths correctly