Further doc updates

bacpop · Aug 7, 2024 · 681a8b5 · 681a8b5
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diff --git a/docs/model_distribution.rst b/docs/model_distribution.rst
@@ -12,7 +12,7 @@ Database contents
 A database requires the following files:
 
 - ``.h5``. The sketch database, a HDF5 file.
-- ``.dists.pkl`` and ``.dists.npy`` files. Distances for all vs all samples in the sketch database.
+- ``.dists.pkl`` file. Order and names of samples in the sketch database.
 - ``_fit.npz`` and ``_fit.pkl`` files. Python files which describe the model fit.
 - ``_graph.gt``. The network relating distances, fit and strain assignment for all samples in the sketch database.
 - ``_clusters.csv``. The strain assignment of all samples in the sketch database.

diff --git a/docs/query_assignment.rst b/docs/query_assignment.rst
@@ -18,7 +18,7 @@ as queries. The clusters assigned by PopPUNK are variable-length-k-mer clusters
 A database called ``database`` will contain the following files, in ``database/``:
 
 - ``database.h5`` -- the sketches of the reference sequences generated by ``pp-sketchlib``.
-- ``database.dists.npy`` and ``database.dists.pkl`` -- the core and accessory distances for
+- ``database.dists.pkl`` -- the order of the core and accessory distances for
   all pairwise comparisons in the sketch database.
 - ``database_fit.npz`` and ``database_fit.pkl`` -- the model fit to the core and accessory distances.
 - ``database_graph.gt`` -- the network defining the fit (loadable with ``graph_tool``).