Refactor SNPObject and improve docstrings

- Rename average_strands to is_phased.
- Add common_variants_intersection to subset_to_common_variants.
- Add common_markers_intersection to subset_to_common_markers.
- Rename filename to file.
- Rename correct_snp_variants to correct_flipped_variants.
- Refine docstrings for improved clarity and consistency.

demos/SNPObj.ipynb

@@ -10,7 +10,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 27,
+   "execution_count": 1,
    "id": "674d136a-1ded-4ce0-babc-87556d518b5f",
    "metadata": {},
    "outputs": [],
@@ -319,7 +319,13 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Unique genotype values before renaming missings: [0 1]\n",
+      "Unique genotype values before renaming missings: [0 1]\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
       "Unique genotype values after renaming missings: [0 1]\n"
      ]
     }
@@ -424,13 +430,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Number of SNPs before filtering by indexes: 976599\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
+      "Number of SNPs before filtering by indexes: 976599\n",
       "Number of SNPs after filtering by indexes: 3\n"
      ]
     }
@@ -466,7 +466,13 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Samples before filtering: ['sample_A', 'sample_B', 'sample_C', 'sample_D']\n",
+      "Samples before filtering: ['sample_A', 'sample_B', 'sample_C', 'sample_D']\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
       "Samples after filtering: ['sample_A', 'sample_B']\n"
      ]
     }
@@ -657,7 +663,7 @@
     }
    ],
    "source": [
-    "snpobj_corrected = snpobj.correct_snp_variants(snpobj2, check_complement=True, index_by='pos', inplace=False)\n",
+    "snpobj_corrected = snpobj.correct_flipped_variants(snpobj2, check_complement=True, index_by='pos', inplace=False)\n",
     "\n",
     "print(\"SNP flips corrected.\")"
    ]
@@ -728,7 +734,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "First 5 variant positions after shuffling: [14258595 13978490 23721180 30763191 42617482]\n"
+      "First 5 variant positions after shuffling: [45903479 41864913 32108927 26948879 19065364]\n"
      ]
     }
    ],
@@ -834,7 +840,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 24,
+   "execution_count": 26,
    "id": "fbca1fd8",
    "metadata": {},
    "outputs": [
@@ -873,7 +879,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 25,
+   "execution_count": 27,
    "id": "cea856ad",
    "metadata": {},
    "outputs": [