Configuration¶

HCRProbeDesign stores reference genome index paths in HCRconfig.yaml. The file is located in the package directory and is read at runtime.

Example¶

species:
  mouse:
    bowtie2_index: indices/mm10/mm10
  human:
    bowtie2_index: /path/to/hg38/index_prefix

Notes¶

• Paths can be absolute or package-relative.
• buildGenomeIndex updates this file automatically.
• fetchMouseIndex also registers the mouse index for you.
• Use --config to write to a different config file when building indices.