From c692f4d41de013bb240cd18b6e20be852ec4ae63 Mon Sep 17 00:00:00 2001
From: Jerome Kelleher <jk@well.ox.ac.uk>
Date: Wed, 15 May 2024 10:14:18 +0100
Subject: [PATCH 1/4] Fix cast paths

---
 docs/vcf2zarr/tutorial.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/vcf2zarr/tutorial.md b/docs/vcf2zarr/tutorial.md
index 7f6dbff..13a79f8 100644
--- a/docs/vcf2zarr/tutorial.md
+++ b/docs/vcf2zarr/tutorial.md
@@ -22,7 +22,7 @@ need for small, intermediate and large datasets.
 
  <div id="vcf2zarr_convert"></div>
  <script>
- AsciinemaPlayer.create('_static/vcf2zarr_convert.cast',
+ AsciinemaPlayer.create('../_static/vcf2zarr_convert.cast',
     document.getElementById('vcf2zarr_convert'), {
     cols:80,
     rows:12
@@ -33,7 +33,7 @@ need for small, intermediate and large datasets.
 
  <div id="vcf2zarr_explode"></div>
  <script>
- AsciinemaPlayer.create('_static/vcf2zarr_explode.cast',
+ AsciinemaPlayer.create('../_static/vcf2zarr_explode.cast',
     document.getElementById('vcf2zarr_explode'), {
     cols:80,
     rows:12

From 91dea48153b4a94069d7c973ecdbf6fb7b7f2c3b Mon Sep 17 00:00:00 2001
From: Jerome Kelleher <jk@well.ox.ac.uk>
Date: Wed, 15 May 2024 12:00:19 +0100
Subject: [PATCH 2/4] Start on documenting vcfpartition

Fixup some issues with running Bash code cells
---
 docs/_config.yml              |  4 ++++
 docs/build.sh                 |  5 +++--
 docs/vcfpartition/overview.md | 37 +++++++++++++++++------------------
 3 files changed, 25 insertions(+), 21 deletions(-)

diff --git a/docs/_config.yml b/docs/_config.yml
index c594a3d..1d4d190 100644
--- a/docs/_config.yml
+++ b/docs/_config.yml
@@ -25,3 +25,7 @@ html:
 sphinx:
   extra_extensions:
     - sphinx_click.ext
+  config:
+    # This is needed to make sure that text is output in single block from
+    # bash cells.
+    nb_merge_streams: true
diff --git a/docs/build.sh b/docs/build.sh
index d454c14..656b523 100755
--- a/docs/build.sh
+++ b/docs/build.sh
@@ -1,4 +1,5 @@
 #/bin/bash
+set -e
 
 # Jupyter-build doesn't have an option to automatically show the 
 # saved reports, which makes it difficult to debug the reasons for 
@@ -11,10 +12,10 @@ RETVAL=$?
 if [ $RETVAL -ne 0 ]; then
     if [ -e $REPORTDIR ]; then
       echo "Error occured; showing saved reports"
-      cat $REPORTDIR/*
+      cat $REPORTDIR/*/*
     fi
 else
     # Clear out any old reports
-    rm -f $REPORTDIR/*
+    rm -fR $REPORTDIR/*
 fi
 exit $RETVAL
diff --git a/docs/vcfpartition/overview.md b/docs/vcfpartition/overview.md
index 6d9dbad..35ab658 100644
--- a/docs/vcfpartition/overview.md
+++ b/docs/vcfpartition/overview.md
@@ -1,3 +1,14 @@
+---
+jupytext:
+  formats: md:myst
+  text_representation:
+    extension: .md
+    format_name: myst
+kernelspec:
+  display_name: Bash
+  language: bash
+  name: bash
+---
 (sec-vcfpartition)=
 # vcfpartition
 
@@ -5,26 +16,14 @@
 
 Partition a given VCF file into (approximately) a give number of regions:
 
-```
-vcf_partition 20201028_CCDG_14151_B01_GRM_WGS_2020-08-05_chr20.recalibrated_variants.vcf.gz -n 10
-```
-gives
-```
-chr20:1-6799360
-chr20:6799361-14319616
-chr20:14319617-21790720
-chr20:21790721-28770304
-chr20:28770305-31096832
-chr20:31096833-38043648
-chr20:38043649-45580288
-chr20:45580289-52117504
-chr20:52117505-58834944
-chr20:58834945-
+
+```{code-cell}
+vcfpartition CEUTrio.20.21.gatk3.4.g.bcf -n 3
 ```
 
-These reqion strings can then be used to split computation of the VCF
-into chunks for parallelisation.
 
-**TODO give a nice example here using xargs**
+```{code-cell}
+vcfpartition CEUTrio.20.21.gatk3.4.g.bcf -n 3 \
+    | xargs -P 3 -I {} sh -c "bcftools view -Hr {} CEUTrio.20.21.gatk3.4.g.bcf | wc -l"
+```
 
-**WARNING that this does not take into account that indels may overlap**

From 7a781764b11a7f4e2a62f229d1d469640450be18 Mon Sep 17 00:00:00 2001
From: Jerome Kelleher <jk@well.ox.ac.uk>
Date: Wed, 15 May 2024 12:02:57 +0100
Subject: [PATCH 3/4] Add bcftools to the docs build

---
 .github/workflows/docs.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index 4098657..0dab5d0 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -31,6 +31,10 @@ jobs:
           pip install -r docs/requirements.txt
           python3 -m bash_kernel.install
 
+      - name: Install bcftools
+        run: |
+          sudo apt-get install bcftools
+
       - name: Install package
         run: |
           python3 -m pip install .

From 81fb76b7333c486e8a8696fb3e116f1980f97624 Mon Sep 17 00:00:00 2001
From: Jerome Kelleher <jk@well.ox.ac.uk>
Date: Wed, 15 May 2024 13:37:08 +0100
Subject: [PATCH 4/4] Fix initialisation

---
 docs/build.sh                 | 1 -
 docs/vcfpartition/overview.md | 4 ++++
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/docs/build.sh b/docs/build.sh
index 656b523..4165d36 100755
--- a/docs/build.sh
+++ b/docs/build.sh
@@ -1,5 +1,4 @@
 #/bin/bash
-set -e
 
 # Jupyter-build doesn't have an option to automatically show the 
 # saved reports, which makes it difficult to debug the reasons for 
diff --git a/docs/vcfpartition/overview.md b/docs/vcfpartition/overview.md
index 35ab658..2efd120 100644
--- a/docs/vcfpartition/overview.md
+++ b/docs/vcfpartition/overview.md
@@ -11,6 +11,10 @@ kernelspec:
 ---
 (sec-vcfpartition)=
 # vcfpartition
+```{code-cell} 
+:tags: [remove-cell]
+cp ../../tests/data/vcf/CEUTrio.20.21.gatk3.4.g.bcf* ./
+```
 
 ## Overview