note on debugging

Author: petrelharp

docs/_toc.yml

@@ -27,6 +27,7 @@ parts:
 - caption: For developers
   chapters:
   - file: development
+  - file: debugging
   - file: changelogs
 - caption: Miscellaneous
   chapters:

docs/debugging.md

@@ -0,0 +1,62 @@
+---
+jupytext:
+  text_representation:
+    extension: .md
+    format_name: myst
+    format_version: 0.12
+    jupytext_version: 1.9.1
+kernelspec:
+  display_name: Python 3
+  language: python
+  name: python3
+---
+
+```{currentmodule} tskit
+```
+
+(sec_debugging)=
+
+# Debugging non-compliant tree sequences
+
+If you're working on an application that writes out tree sequences
+(or more properly, the underlying table collections),
+you may find yourself in the situation where you're writing out files
+that tskit cannot read because of violations of the {ref}`sec_data_model`.
+How to see what's going on?
+
+First, try loading the {class}`.TableCollection` directly (skipping
+the convert-to-tree-sequence step that involves additional validation).
+This will work if you have errors like a mutation that references a
+non-extant node, for instance.
+To do this, you simply run:
+```{code-cell} python
+import tskit
+tables = tskit.TableCollection.load("data/basic_tree_seq.trees")
+print(tables)
+```
+Then, the tables can be inspected.
+
+Sometimes the error makes it so the tables cannot even be loaded
+as a {class}`.TableCollection`: for instance, if something went wrong
+with the {ref}`ragged columns<sec_encoding_ragged_columns>`.
+Under the hood, data is stored on disk
+with [kastore](https://github.com/tskit-dev/kastore),
+so we can use kastore directly:
+```{code-cell} python
+import kastore
+ka = kastore.load("data/basic_tree_seq.trees")
+print(ka)
+```
+The kastore has (by design!) very minimal functionality:
+we can ask what *keys* it has, and retrieve the associated values.
+So, this one has these keys:
+```{code-cell} python
+list(ka.keys())
+```
+The names are self-explanatory.
+For instance, we can look at the array of child nodes associated with each edge:
+```{code-cell} python
+ka.get("edges/child")
+```
+
+Good luck!