Add n mapped and total reads to results.json

report.ipynb

@@ -111,7 +111,7 @@
    "outputs": [],
    "source": [
     "samtools_view_output = !samtools view -F 4 $BAM_PATH | wc -l\n",
-    "n_aligned_reads = int(samtools_view_output[0])"
+    "n_mapped_reads = int(samtools_view_output[0])"
    ]
   },
   {
@@ -216,7 +216,7 @@
     "This report summarizes the detection of SARS-CoV-2, the causative agent of COVID-19, in sample \n",
     "<strong>{sample_filename}</strong>. \n",
     "This sample contained <strong>{n_reads:,}</strong> reads, with\n",
-    "<strong>{n_aligned_reads:,}</strong> mapping to the \n",
+    "<strong>{n_mapped_reads:,}</strong> mapping to the \n",
     "<a href='https://www.ncbi.nlm.nih.gov/nuccore/MN908947.3/' target='_blank'>reference</a>. \n",
     "Reads cover <strong>{cov:.0%}</strong> of the genome ({cov_10x:.0%} over 10×), with a mean depth of <strong>{depth:.1f}×</strong>.\n",
     "A total of <strong>{n_snps}</strong> variant{'s were' if n_snps != 1 else 'was'} detected.\"\"\"\n",
@@ -345,6 +345,8 @@
    "source": [
     "# Save a JSON too, including filtered variants <10x\n",
     "results = {\n",
+    "    \"n_reads\": n_reads,\n",
+    "    \"n_mapped_reads\": n_mapped_reads,\n",
     "    \"report_id\": os.environ.get(\"ONE_CODEX_REPORT_UUID\"), \n",
     "    \"sample_id\": os.environ.get(\"ONE_CODEX_SAMPLE_UUID\"),\n",
     "    \"variants\": [r.to_dict() for _, r in snp_table.iterrows()]\n",