finish up genomicranges section

BiocPy · Jan 12, 2024 · cdb2495 · cdb2495
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diff --git a/_quarto.yml b/_quarto.yml
@@ -22,8 +22,10 @@ book:
     - part: chapters/representations/index.qmd
       chapters:
         - chapters/representations/biocframe.qmd
-        - chapters/representations/iranges.qmd
         - chapters/representations/genomicranges.qmd
+    - part: chapters/extras/index.qmd
+      chapters:
+        - chapters/extras/iranges.qmd
     - chapters/summary.qmd
     - chapters/references.qmd
 

diff --git a/chapters/extras/index.qmd b/chapters/extras/index.qmd
@@ -0,0 +1 @@
+# Additional packages
diff --git a/chapters/representations/iranges.qmd → chapters/extras/iranges.qmd b/chapters/representations/iranges.qmd → chapters/extras/iranges.qmd
@@ -1,9 +1,12 @@
-# `IRanges`: Interval arithmetic
+# `IRanges`: Interval arithmetic {.unnumbered}
 
 Python implementation of the [**IRanges**](https://bioconductor.org/packages/IRanges) Bioconductor package.
 
+An `IRanges` holds a **start** position and a **width**, and is typically used to represent coordinates along a genomic sequence. The interpretation of the **start** position depends on the application; for sequences, the **start** is usually a 1-based position, but other use cases may allow zero or even negative values, e.g., circular genomes. 
 
-## Installation
+`IRanges` uses [nested containment lists](https://github.com/pyranges/ncls) under the hood to perform fast overlap and search based operations. 
+
+## Installation {#sec-iranges}
 To get started, install the package from [PyPI](https://pypi.org/project/IRanges/)
 
 ```bash
@@ -171,6 +174,8 @@ intersection = x.intersect(y)
 print(intersection)
 ```
 
+----
+
 ## Further reading
 
 - [IRanges reference](https://biocpy.github.io/IRanges/api/iranges.html#iranges-package)

diff --git a/chapters/representations/biocframe.qmd b/chapters/representations/biocframe.qmd
@@ -170,7 +170,7 @@ print(out)
 
 ## Extracting data
 
-BiocPy classes follow a functional paradigm for accessing or setting properties, with further details available in [@sec-functional].
+BiocPy classes follow a functional paradigm for accessing or setting properties, with further details discussed in [functional paragidm](@sec-functional) section.
 
 Properties can be directly accessed from the object:
 
@@ -366,7 +366,7 @@ print("\nSubsetting an empty BiocFrame: \n", subset_empty)
 
 ----
 
-## Notes
+## Further reading
 
 Check out [the reference documentation](https://biocpy.github.io/BiocFrame/) for more details.