Updating to match the current version of vg giraffe's use of zipcodes in indexing

Author: joannmudge

module_notebooks/05-indexing-graphs-with-vg.ipynb

@@ -230,9 +230,11 @@
     "\n",
     "A. *yprp.chrVIII.pggb.giraffe.gbz* - a [GBZ](https://academic.oup.com/bioinformatics/article/38/22/5012/6731924?login=false) format graph that includes a [GBWT](https://github.com/jltsiren/gbwt) index and the corresponding GBWTGraph.\n",
     "\n",
-    "B. *yprp.chrVIII.pggb.min* - minimizer index annotated with positions in the distance index.\n",
+    "B. *yprp.chrVIII.pggb.shortread.withzip.min* - minimizer index annotated with positions in the distance index.\n",
     "\n",
-    "C. *yprp.chrVIII.pggb.dist* - minimum distance index.\n"
+    "C. *yprp.chrVIII.pggb.shortread.zipcodes* - zipcode file (distance hints).\n",
+    "\n",
+    "D. *yprp.chrVIII.pggb.dist* - minimum distance index.\n"
    ]
   },
   {
@@ -300,7 +302,9 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "jp-MarkdownHeadingCollapsed": true
+   },
    "source": [
     "----------------------\n",
     "\n",
@@ -423,8 +427,14 @@
   }
  ],
  "metadata": {
+  "environment": {
+   "kernel": "conda-env-nigms-pangenomics-nigms-pangenomics",
+   "name": "workbench-notebooks.m127",
+   "type": "gcloud",
+   "uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m127"
+  },
   "kernelspec": {
-   "display_name": "nigms-pangenomics (Local)",
+   "display_name": "nigms-pangenomics",
    "language": "python",
    "name": "conda-env-nigms-pangenomics-nigms-pangenomics"
   },

module_notebooks/06-read-mapping-with-vg.ipynb

@@ -186,9 +186,11 @@
     "\n",
     "The parameters:  \n",
     "\n",
+    "`-p`  show progress  \n",
     "`-Z`  .gbz file  \n",
     "`-m`  .min file  \n",
-    "`-d`  .dist file\n",
+    "`-z`  zipcode file  \n",
+    "`-d`  .dist file  \n",
     "`-f`  fastq file (use more than once if feeding in paired-end read files)\n",
     "\n",
     "We will redirect the output into a gam file."
@@ -200,7 +202,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "!vg giraffe -p -Z graphs/yprp.chrVIII.pggb.giraffe.gbz -m graphs/yprp.chrVIII.pggb.min -d graphs/yprp.chrVIII.pggb.dist -f reads/SK1.illumina_1.fastq.gz -f reads/SK1.illumina_2.fastq.gz > alignments/SK1xyprp.chrVIII.pggb.mapped.gam"
+    "!vg giraffe -p -Z graphs/yprp.chrVIII.pggb.giraffe.gbz -m graphs/yprp.chrVIII.pggb.shortread.withzip.min -z graphs/yprp.chrVIII.pggb.shortread.zipcodes -d graphs/yprp.chrVIII.pggb.dist -f reads/SK1.illumina_1.fastq.gz -f reads/SK1.illumina_2.fastq.gz > alignments/SK1xyprp.chrVIII.pggb.mapped.gam"
    ]
   },
   {
@@ -509,8 +511,14 @@
   }
  ],
  "metadata": {
+  "environment": {
+   "kernel": "conda-env-nigms-pangenomics-nigms-pangenomics",
+   "name": "workbench-notebooks.m127",
+   "type": "gcloud",
+   "uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m127"
+  },
   "kernelspec": {
-   "display_name": "nigms-pangenomics (Local)",
+   "display_name": "nigms-pangenomics",
    "language": "python",
    "name": "conda-env-nigms-pangenomics-nigms-pangenomics"
   },