test for edge edit

tests/integration_tests.ipynb

@@ -2889,14 +2889,25 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 4,
    "id": "f5c3ed3e-13dd-4399-924e-3d1ac17ce387",
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
+      "\n",
+      "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n",
+      "Checking results for edge_case_test\n",
+      "\tExpecting: {'contig': '10', 'barcode': 'AAACGAATCATTCATC-1', 'position': 132330481, 'num_rows': 1, 'count': 1, 'coverage': 1, 'conversion': 'T>G', 'strand_conversion': 'A>C', 'strand': '-', 'feature_name': 'STK32C', 'feature_strand': '-'}\n",
+      "\n",
+      "\t >>> edge_case_test passed! <<<\n",
+      "\n",
+      "\tExpecting: {'contig': '10', 'barcode': 'AAACGAATCATTCATC-1', 'position': 132330438, 'num_rows': 1, 'count': 1, 'coverage': 1, 'conversion': 'T>C', 'strand_conversion': 'A>G', 'strand': '-', 'feature_name': 'STK32C', 'feature_strand': '-'}\n",
+      "\n",
+      "\t >>> edge_case_test passed! <<<\n",
+      "\n",
       "\n",
       "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n",
       "Checking results for unstranded_pair_test\n",
@@ -2992,21 +3003,38 @@
     }
    ],
    "source": [
+    "import pandas as pd\n",
+    "\n",
     "test_name_to_expectations = {\n",
     "    \"edge_case_test\": {\n",
     "        \"folder\": \"singlecell_tests\",\n",
-    "        \"annotated\": False,\n",
     "        \"expectations\": [{\n",
     "            \"contig\": \"10\",\n",
-    "            \"barcode\": \t\"GGGACCTTCGAGCCAC-1\",\n",
-    "            \"position\": 3000524,\n",
+    "            \"barcode\": \t\"AAACGAATCATTCATC-1\",\n",
+    "            \"position\": 132330481,\n",
     "            \"num_rows\": 1,\n",
     "            \"count\": 1,\n",
-    "            \"coverage\": 12,\n",
-    "            \"conversion\": \"C>A\",\n",
-    "            \"strand_conversion\": \"G>T\",\n",
-    "            \"strand\": \"-\"\n",
-    "        }]\n",
+    "            \"coverage\": 1,\n",
+    "            \"conversion\": \"T>G\",\n",
+    "            \"strand_conversion\": \"A>C\",\n",
+    "            \"strand\": \"-\",\n",
+    "            \"feature_name\": \"STK32C\",\n",
+    "            \"feature_strand\": \"-\"\n",
+    "        },\n",
+    "        {\n",
+    "            \"contig\": \"10\",\n",
+    "            \"barcode\": \t\"AAACGAATCATTCATC-1\",\n",
+    "            \"position\": 132330438,\n",
+    "            \"num_rows\": 1,\n",
+    "            \"count\": 1,\n",
+    "            \"coverage\": 1,\n",
+    "            \"conversion\": \"T>C\",\n",
+    "            \"strand_conversion\": \"A>G\",\n",
+    "            \"strand\": \"-\",\n",
+    "            \"feature_name\": \"STK32C\",\n",
+    "            \"feature_strand\": \"-\"\n",
+    "        }\n",
+    "                        ]\n",
     "    },\n",
     "    \"unstranded_pair_test\": {\n",
     "        \"folder\": \"strandedness_tests\",\n",

tests/integration_tests_auto_check.py

@@ -2,6 +2,36 @@
 import sys
 
 test_name_to_expectations = {
+    "edge_case_test": {
+        "folder": "singlecell_tests",
+        "expectations": [{
+            "contig": "10",
+            "barcode": 	"AAACGAATCATTCATC-1",
+            "position": 132330481,
+            "num_rows": 1,
+            "count": 1,
+            "coverage": 1,
+            "conversion": "T>G",
+            "strand_conversion": "A>C",
+            "strand": "-",
+            "feature_name": "STK32C",
+            "feature_strand": "-"
+        },
+        {
+            "contig": "10",
+            "barcode": 	"AAACGAATCATTCATC-1",
+            "position": 132330438,
+            "num_rows": 1,
+            "count": 1,
+            "coverage": 1,
+            "conversion": "T>C",
+            "strand_conversion": "A>G",
+            "strand": "-",
+            "feature_name": "STK32C",
+            "feature_strand": "-"
+        }
+                        ]
+    },
     "unstranded_pair_test": {
         "folder": "strandedness_tests",
         "expectations": [{
@@ -132,7 +162,7 @@
         }]
     },
 
-        "only_5_cells_test": {
+    "only_5_cells_test": {
         "folder": "singlecell_tests",
         "expectations": [{
             "contig": "9",

tests/integration_tests_run.sh

@@ -34,7 +34,7 @@ echo "SC tests scripts"
 ls -lh $MARINE/tests/$tests_folder/scripts/
 
 
-for t in "only_5_cells_test" "long_read_sc_test"
+for t in "only_5_cells_test" "long_read_sc_test" "edge_case_test"
 
 do
     echo $t

tests/singlecell_tests/scripts/edge_case_test.sh

@@ -0,0 +1,30 @@
+# This sample has an edit at the very end of the read. It's a good test to ensure that we don't have off by one errors
+# in computing the coverage. It was aligned to the craig venter genome, so the reference is slightly difference from
+# hg38 -- if aligning with hg38, this read doesn't have mutations at these positions.
+
+# Expected edit
+# AAACGAATCATTCATC-1      10_AAACGAATCATTCATC-1   10_AAACGAATCATTCATC-1:132330481 132330481       T       G       A00621:106:HLFHGDSXX:3:1152:16830:27352 -
+
+# Expected combined.bed file
+# 10_AAACGAATCATTCATC-1	132330438	132330439
+# 10_AAACGAATCATTCATC-1	132330481	132330482
+
+# Read
+# A00621:106:HLFHGDSXX:3:1152:16830:27352 16      10_AAACGAATCATTCATC-1   132330391       255     91M     *       0       0       GCAACACCCATGTCACTCCTCATTCTCTCCTTGCTCTGCCCGGGTGGCTGGCCTCCCCACGCTCCTGAGAAGGTACTGGTTGTGCTTTCAG     FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF    NH:i:1   HI:i:1  AS:i:89 nM:i:0  TX:Z:ENST00000456004,+406,91M   GX:Z:ENSG00000165752    GN:Z:STK32C     fx:Z:ENSG00000165752    RE:A:E  li:i:0  BC:Z:TTTCCACT  QT:Z:FFFFF:FF    CR:Z:AAACGAATCATTCATC   CY:Z:FFFFFFFFFFFFFFFF   CB:Z:AAACGAATCATTCATC-1 UR:Z:CGCTTAAAACCT       UY:Z:FFFFFFFFFFFF       UB:Z:CGCTTAAAACCT      xf:i:25  RG:Z:10X214_1_AB_1:0:1:HLFHGDSXX:3      NM:i:2  MD:Z:47T42T0
+
+mypython=$1
+
+$mypython $MARINE/marine.py \
+--bam_filepath \
+$MARINE/tests/singlecell_tests/bams/10_C-1_orig.bam \
+--annotation_bedfile_path \
+$MARINE/annotations/cellranger-GRCh38-3.0.0.annotation.genes.bed \
+--output_folder \
+$MARINE/tests/singlecell_tests/edge_case_test \
+--min_base_quality \
+15 \
+--cores \
+4 \
+--barcode_tag "CB" \
+--strandedness 2 --num_per_sublist 1 --verbose \
+--contigs 10 --interval_length 40000000 --keep_intermediate_files