meRanTK_v1.3.0

Version 1.3.0

• meRanCall:
  Implemented a C-cutoff filter. Removes reads from poor conversion
  in the sense that if a read has more than C_cutoff Cs it will
  not be considered in m5C calling.
  Implement signal to noise ratio filter. Only consider sites
  that have a SNR higher than signalToNoise
  Implement a minimum C filter. Only consider sites that hav a
  minimum of minC Cs.

  Implemented gene level CR. meRanCall can now calculate the CR for
  each individual gene from a provided GTF file. This CR is than
  used in the statistical tests for the candidate sites in a
  corresponding gene.

  Implemented conflict solving for overlapping mates of a read pair.
  Only one base call, namely the one of the mate with the better
  quality score, is considered.

• updated third party programs: STAR, HiSat2, bowtie2

• provide a conda env YML file for meRanTK

• added support for the current RefSeq mRNA fasta files from NCBI
  in the mkRefSeq2GeneMap.pl utility.

• minor fixes