Merge pull request #197 from jeromekelleher/improve-casts2

More cast updates

Author: jeromekelleher

docs/Makefile

@@ -3,12 +3,16 @@ PYPATH=$(shell pwd)/../
 B2Z_VERSION:=$(shell PYTHONPATH=${PYPATH} \
    python3 -c 'import bio2zarr; print(bio2zarr.__version__.split("+")[0])')
 
+CASTS=_static/vcf2zarr_convert.cast\
+	_static/vcf2zarr_explode.cast
+
+
 BUILDDIR      = _build
 
-dev: _static/vcf2zarr_convert.cast
+dev: ${CASTS}
 	PYTHONPATH=${PYPATH} ./build.sh
 
-dist: _static/vcf2zarr_convert.cast
+dist: ${CASTS}
 	@echo Building distribution for bio2zarr version ${B2Z_VERSION}
 	cd doxygen && doxygen
 	sed -i -e s/__BIO2ZARR_VERSION__/${B2Z_VERSION}/g _config.yml
@@ -18,8 +22,15 @@ clean:
 	rm -fR $(BUILDDIR)
 
 
-_static/vcf2zarr_convert.cast:
-	rm -fR sample.zarr
+sample.vcf.gz:
 	cp ../tests/data/vcf/sample.vcf.gz ./
 	cp ../tests/data/vcf/sample.vcf.gz.tbi ./
-	asciinema-automation cast_scripts/vcf2zarr_convert.sh _static/vcf2zarr_convert.cast
+
+_static/vcf2zarr_convert.cast: sample.vcf.gz
+	rm -f sample.vcz
+	asciinema-automation cast_scripts/vcf2zarr_convert.sh $@
+
+_static/vcf2zarr_explode.cast: sample.vcf.gz
+	rm -Rf sample.icf
+	asciinema-automation cast_scripts/vcf2zarr_explode.sh $@
+

docs/cast_scripts/vcf2zarr_convert.sh

@@ -1,3 +1,3 @@
-#$ delay 10
-vcf2zarr convert sample.vcf.gz sample.zarr -p 4
+#$ delay 5
+vcf2zarr convert sample.vcf.gz sample.vcz
 #$ expect \$ 

docs/cast_scripts/vcf2zarr_explode.sh

@@ -0,0 +1,3 @@
+#$ delay 5
+vcf2zarr explode sample.vcf.gz sample.icf 
+#$ expect \$ 

docs/vcf2zarr/tutorial.md

@@ -20,10 +20,6 @@ need for small, intermediate and large datasets.
 
 ## Small
 
-<!-- ```{code-cell} bash -->
-<!-- vcf2zarr convert ../tests/data/vcf/sample.vcf.gz sample.zarr -vf -->
-<!-- ``` -->
-
  <div id="vcf2zarr_convert"></div>
  <script>
  AsciinemaPlayer.create('_static/vcf2zarr_convert.cast',
@@ -35,5 +31,15 @@ need for small, intermediate and large datasets.
 
 ## Intermediate
 
+ <div id="vcf2zarr_explode"></div>
+ <script>
+ AsciinemaPlayer.create('_static/vcf2zarr_explode.cast',
+    document.getElementById('vcf2zarr_explode'), {
+    cols:80,
+    rows:12
+ });
+ </script>
+
+
 ## Large