0.3.5

• code cleanup

0.3.4

• add STAR param limitGenomeGenerateRAM to config

0.3.3

• support python3 also in requantify.py
• support tsv and csv input files
• remove hard-coded script path from config file

0.3.2

• python 3 support
• allow .csv and tab-separated input tables

0.3.1

• fix error when no reads are mapped to a given input sequence

0.3.0

• Changes on how reads are counted:
  • for junction reads require exact match in regions of interest (+/- bp_dist around input position)
  • Changed STAR command to
    • allow only 5% mismatches relative to alignment length and read length
    • output NM and MD tag in BAM file (need for exact match requirement)
      interest)
• Changes that might affect runtime:
  • cash all reads before counting (this might need to be improved)
• Changes in output format:
  • output file is now tab-delimited and columns are in different order as before
• Add bash scripts to
  • run STAR alignment for example data
  • run BWA alignment for example data

0.2.0

• add an option -d for junction read overlap threshold and change the default to 10bp

0.1.0

• first release of easyquant