Changelog

• V 1.5.3.1: updated to latest GHC pedantic compilation
• V 1.5.3: Upgraded to sequence-formats 1.7.0 introducing an option for plink popName encoding, and improved pileup-Parsing to allow for skip-reference characters
• V 1.5.2: Fixed a bug with --samplePopName having to be entered after -p or -e. Fixed a bug in the sequence-formats dependency.
• V 1.5.1: Added automatic building
• V 1.5.0: Added support for Plink output
• V 1.4.0.4:
  • Fixed eigenstrat-output in pileupCaller to add a dot after the outputprefix before the file extensions.
  • Updated haskell-stack wrapper scripts for EIGENSOFT and ADMIXTOOLS.
  • Moved unmaintained scripts into unmaintained folder.
• V 1.4.0.3: Updated to new sequence-formats version, now including reading of genetic position from eigenstrat files.
• V 1.4.0.1: Improved README, fixed output bug in genoStats.hs
• V 1.4.0: Added single strand mode, and new triallelic treatment.
• V 1.3.1: Bumped dependency on sequence-formats to new sequence-formats-1.4.0, which includes strand-information in pileup data, as well as rsIds in freqSum to output the correct rsId, and an option to parse chromosomes X, Y and MT.
• V 1.3.0: Lots of refactoring. Lots of testing. Removed some features in vcf2eigenstrat and in pileupCaller, including the option in pileupCaller to call without a SNP file.
• V 1.2.4: normaliseBimWithVCF is ready.
• V 1.2.3 : Adapted to newest sequence-formats. Had to change all the chromosome-related code to the newType Chrom datatype. Also started implementing normaliseBimWithVCF.