HATCHet v0.3.3

This HATCHet release fixes a couple of bugs, especially when running the end-end HATCHET run command with a workflow .ini file.

• Fixed a possible AssertionError: Samples in BBC files does not match the ones in SEG file! in the compute-cn step (had to do with the cluster-bins step failing to close the .seg/.bbc files properly.
• A pre-downloaded SNP file specified as the genotype_snps.snps key in the .ini file would have been ignored. This is now fixed.
• The --baseCN argument for the plot-cn step, when explicitly specified on the command line, caused an error due to incorrect typecasting. This is now fixed.

HATCHet v0.3.2

This version fixes a "missing reference genome" bug with the count_reads step of the HATCHet pipeline, when run using the hatchet run <inifile> command.

HATCHet v0.3.1

When many clusters are selected (e.g. if no cluster size selection criteria is given), still select the largest clusters based on the number of colors in the palette to ensure they get assigned a color. All other clusters get colored gray.

A -V or --version flag is available on all HATCHet commands.

HATCHet 0.3.0

This version of hatchet renames all HATCHet commands (old commands are still supported), and introduces a top-level hatchet run command that can run HATCHet end-end.

HATCHet 0.2.11

This release adds some helper scripts in the $CONDA_PREFIX/bin folder for easy usage of HATCHet when installed directly from bioconda.

• hatchet_unphased
• hatchet_phased_1
• hatchet_phased_2
• hatchet_config (for fine-tuning the other 3 scripts)

Python 3

Experimental release to check for bioconda integration

First full release

v0.1

Fix threshol in clonal identification