Merge pull request #210 from jeromekelleher/docs-more-docs

More docs infrastructure

.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 .

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

docs/build.sh

@@ -11,10 +11,10 @@ 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

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

docs/vcfpartition/overview.md

@@ -1,30 +1,33 @@
+---
+jupytext:
+  formats: md:myst
+  text_representation:
+    extension: .md
+    format_name: myst
+kernelspec:
+  display_name: Bash
+  language: bash
+  name: bash
+---
 (sec-vcfpartition)=
 # vcfpartition
+```{code-cell} 
+:tags: [remove-cell]
+cp ../../tests/data/vcf/CEUTrio.20.21.gatk3.4.g.bcf* ./
+```
 
 ## Overview
 
 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**