Mason 2 TODOs
=============

URGENT
------

mason_simulator

 * FASTQ input from a typical run for quality and N-patterns, cycle through data
   - This requires bulk-simulation of reads to circumvent possible problems.

mason_splicer

 * test splicing on dmel, check by blasting against reference

IMPORTANT
---------

 * testing, FASTQ profiles etc., methylation pattern check
 * joining of FASTA files uses lexical comparison not natural number order
 * exceptions instead of return codes
 * use different seeds from command line for methylation levels and other stuff
 * rework methylation simulation with context (drop C context, cannot happen!)

LATER
-----

 * biases in mismatch errors from input, trained from real-world data
 * add simulation of adaptors/barcodes
 * more robust parsing of VCF for variant import
