• Added –pepper option to for permissive pileups by overriding the pysam pileup stepper to all instead of samtools.


  • Move process_vcf to util module. I may drop use of pyvcf in future as I don’t like the API.
  • Dropped pointless append_path stub.
  • Fixed an edge case where reads beginning with a SNP that aligned to the start of a parallel parsing window are counted twice.
  • Added a small test package to help detect future regressions.
  • Added –version argument to print program version number.
  • Removed –lorder argument as users should not need to select the chain order.


  • Adds –dumpmatrix and –dumpsnps debugging options.
  • Clean up Hansel matrix initialisation.
  • Add gretel-snpper command for generating naive VCF.
  • Fix a regression where the L parameter of the matrix is incorrectly left unset.


Resolves a bug whereby SNPs are incorrectly parsed from the BAM if either:
  • its quality score is below 13
  • the read is overlapped by its primary mate

Well covered data sets need not be overly affected by the additional noise that may have been introduced, but the problem is more noticeable with low coverage and you may wish to reapply Gretel to affected data. Sorry.


  • Add warning and advice when an entry in Hansel is missing evidence.
  • Make the ‘Unable to select’ warning sound much less bad because it is normal.


  • Docs
  • Deprecate gretel-crumbs command


  • Further improvements to parallel read processing
  • Add - symbol to enable support for deletions


  • Fix setting of L parameter


  • Re-write read handling, again


  • -s and -e introduced to allow specification of positions between which to recover haplotypes
  • Attempt some basic indel handling
  • Fix a bug where the master sequence was altered by the output of each reported haplotype


  • Add experimental –sentinels option
  • Improve docs


  • Hansel is now seperate from Gretel
  • [Hansel] get_marginal_at is now get_counts_at
  • [Hansel] selext_next_edge_at deprecated
  • Gene recovery and likelihood plots are now on seperate panels
  • Re-write methods to add observations to matrix to be less awful to read
  • Drop –hit and –gene options to verification
  • Replace verification script to gretel-crumbs command


  • Improve documentation.
  • Provide util subpackage for filling Hansel structure with BAM observations.
  • Explicitly provide possible symbols to Hansel.
  • Improve plotting
  • Remove process_hits and process_refs as these are no longer needed.
  • Rename establish_path to generate_path
  • Rename add_ignore_support3 to reweight_hansel_from_graph so we have some sort of indication of what it does.
  • Altered Sphinx configuation.


  • Import repository from claw.