BiNgoViewer 2.3.4__tar.gz → 2.4.0__tar.gz

{bingoviewer-2.3.4 → bingoviewer-2.4.0}/BiNgoViewer.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: BiNgoViewer
-Version: 2.3.4
+Version: 2.4.0
 Summary: BiNgo Genome Viewer — a lightweight browser-based genomics viewer
 Author-email: Billy M Ngo <billy.ngo0108@gmail.com>
 License: Proprietary
@@ -11,13 +11,14 @@ Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Science/Research
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Classifier: Programming Language :: Python :: 3.14
 Classifier: Operating System :: OS Independent
-Requires-Python: >=3.10
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 Requires-Dist: fastapi<1.0,>=0.111.0
 Requires-Dist: uvicorn<1.0,>=0.29.0
@@ -101,6 +102,7 @@ Then open [http://localhost:8000](http://localhost:8000).
 | Problem | Solution |
 |---------|----------|
 | `python` not found | Install Python 3.10+ and check **Add to PATH** during setup |
+| "No matching distribution" | Your Python is too old — BiNgo requires **Python 3.10+**. Check with `python --version` |
 | pip install fails | Try `pip install --user BiNgoViewer` or use a virtual environment |
 | Port 8000 in use | Run `bingo --port 9000` (or any free port) |
 | Browser doesn't open | Visit `http://localhost:8000` manually |

{bingoviewer-2.3.4 → bingoviewer-2.4.0}/BiNgoViewer.egg-info/SOURCES.txt

@@ -12,7 +12,7 @@ bingoviewer/cli.py
 bingoviewer/icon.py
 bingoviewer/install_shortcut.py
 bingoviewer/frontend_dist/index.html
-bingoviewer/frontend_dist/assets/index-Dbtbm6Rs.js
+bingoviewer/frontend_dist/assets/index-v6csp4Bc.js
 bingoviewer/server/__init__.py
 bingoviewer/server/main.py
 bingoviewer/server/state.py

{bingoviewer-2.3.4 → bingoviewer-2.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: BiNgoViewer
-Version: 2.3.4
+Version: 2.4.0
 Summary: BiNgo Genome Viewer — a lightweight browser-based genomics viewer
 Author-email: Billy M Ngo <billy.ngo0108@gmail.com>
 License: Proprietary
@@ -11,13 +11,14 @@ Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Science/Research
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Classifier: Programming Language :: Python :: 3.14
 Classifier: Operating System :: OS Independent
-Requires-Python: >=3.10
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 Requires-Dist: fastapi<1.0,>=0.111.0
 Requires-Dist: uvicorn<1.0,>=0.29.0
@@ -101,6 +102,7 @@ Then open [http://localhost:8000](http://localhost:8000).
 | Problem | Solution |
 |---------|----------|
 | `python` not found | Install Python 3.10+ and check **Add to PATH** during setup |
+| "No matching distribution" | Your Python is too old — BiNgo requires **Python 3.10+**. Check with `python --version` |
 | pip install fails | Try `pip install --user BiNgoViewer` or use a virtual environment |
 | Port 8000 in use | Run `bingo --port 9000` (or any free port) |
 | Browser doesn't open | Visit `http://localhost:8000` manually |

{bingoviewer-2.3.4 → bingoviewer-2.4.0}/README.md

@@ -73,6 +73,7 @@ Then open [http://localhost:8000](http://localhost:8000).
 | Problem | Solution |
 |---------|----------|
 | `python` not found | Install Python 3.10+ and check **Add to PATH** during setup |
+| "No matching distribution" | Your Python is too old — BiNgo requires **Python 3.10+**. Check with `python --version` |
 | pip install fails | Try `pip install --user BiNgoViewer` or use a virtual environment |
 | Port 8000 in use | Run `bingo --port 9000` (or any free port) |
 | Browser doesn't open | Visit `http://localhost:8000` manually |

{bingoviewer-2.3.4 → bingoviewer-2.4.0}/bingoviewer/__init__.py

@@ -1,3 +1,3 @@
 """BiNgo Genome Viewer — a lightweight browser-based genomics viewer."""
 
-__version__ = "2.3.4"
+__version__ = "2.4.0"

{bingoviewer-2.3.4 → bingoviewer-2.4.0}/bingoviewer/cli.py

@@ -376,8 +376,16 @@ def _offer_shortcut_install():
     try:
         answer = input("  Create a desktop shortcut? [Y/n]: ").strip()
         if answer.lower() != 'n':
-            from bingoviewer.install_shortcut import main as install_main
-            install_main()
+            try:
+                from bingoviewer.install_shortcut import main as install_main
+                install_main()
+            except ImportError:
+                print("  Shortcut creation requires tkinter.")
+                print("  Install it with: conda install tk  (or)  sudo apt install python3-tk")
+                print("  You can create a shortcut later with: bingo --install")
+            except Exception as e:
+                print(f"  Shortcut creation failed: {e}")
+                print("  You can try again later with: bingo --install")
         return
     except (EOFError, OSError):
         pass
@@ -437,8 +445,14 @@ def main():
         return 0
 
     if args.install:
-        from bingoviewer.install_shortcut import main as install_main
-        install_main()
+        try:
+            from bingoviewer.install_shortcut import main as install_main
+            install_main()
+        except ImportError:
+            print("  Shortcut creation requires tkinter.")
+            print("  Install it with: conda install tk  (or)  sudo apt install python3-tk")
+        except Exception as e:
+            print(f"  Shortcut creation failed: {e}")
         return 0
 
     # ── Manual update command ────────────────────────────────────

bingoviewer-2.3.4/bingoviewer/frontend_dist/assets/index-Dbtbm6Rs.js → bingoviewer-2.4.0/bingoviewer/frontend_dist/assets/index-v6csp4Bc.js

@@ -94,4 +94,4 @@ ${z.join(`
 `)}
 
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",s.jsx("em",{children:"Nature Biotechnology"}),", 29(1), 24","–","26."]}),s.jsx("div",{style:{fontWeight:600,color:e.textPrimary,marginTop:12,marginBottom:4},children:"Acknowledgments"}),s.jsx("div",{children:"Early version testing and feedback:"}),s.jsx("div",{children:"Amanda Antoch, Isaac Poarch, Otto Chipashvili, Jake Colautti"})]})]}),s.jsx("div",{style:{textAlign:"right"},children:s.jsx("button",{onClick:()=>$(!1),style:{background:e.btnBg,border:`1px solid ${e.borderStrong}`,borderRadius:4,color:e.btnText,padding:"5px 18px",cursor:"pointer",fontSize:12,fontWeight:600},children:"Close"})})]})}),F&&(()=>{const B=F.files.length>1,q=F.files.map(X=>X.name).join(", ");return s.jsx("div",{style:{position:"fixed",inset:0,background:"rgba(0,0,0,0.45)",display:"flex",alignItems:"center",justifyContent:"center",zIndex:9999},children:s.jsxs("div",{style:{background:e.panelBg,border:`1px solid ${e.borderAccent}`,borderRadius:8,padding:"20px 24px",maxWidth:440,width:"90%",boxShadow:"0 8px 32px rgba(0,0,0,0.5)"},onClick:X=>X.stopPropagation(),children:[s.jsxs("div",{style:{fontSize:14,fontWeight:700,color:e.textPrimary,marginBottom:8},children:["Genome file",B?"s":""," detected"]}),s.jsxs("div",{style:{fontSize:12,color:e.textSecondary,lineHeight:1.6,marginBottom:16},children:[s.jsx("strong",{style:{color:e.textPrimary},children:q}),B?" appear to be genome files. 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{bingoviewer-2.3.4 → bingoviewer-2.4.0}/bingoviewer/frontend_dist/index.html

@@ -10,7 +10,7 @@
       body { font-family: Arial, Helvetica, sans-serif; background: #1a1a1a; color: #e0e0e0; height: 100vh; overflow: hidden; }
       #root { height: 100vh; display: flex; flex-direction: column; }
     </style>
-    <script type="module" crossorigin src="/assets/index-Dbtbm6Rs.js"></script>
+    <script type="module" crossorigin src="/assets/index-v6csp4Bc.js"></script>
   </head>
   <body>
     <div id="root"></div>

{bingoviewer-2.3.4 → bingoviewer-2.4.0}/bingoviewer/server/api/genome.py

@@ -73,7 +73,10 @@ async def add_chromosomes(file: UploadFile = File(...)):
 async def load_genome_from_path(path: str = Form(...)):
     """Load genome from a local file path."""
     from pathlib import Path as P
-    path = path.strip().strip('"').strip("'").replace('\\ ', ' ')
+    path = path.strip()
+    for q in ('"', "'", '`'):
+        path = path.strip(q)
+    path = path.strip().replace('\\ ', ' ')
     p = P(path).expanduser()
     if not p.exists() and not p.resolve().exists():
         parent = p.parent

{bingoviewer-2.3.4 → bingoviewer-2.4.0}/bingoviewer/server/api/tracks.py

@@ -94,8 +94,12 @@ async def load_track_from_path(path: str = Form(...), name: str = Form("")):
     """Load track from a local file path (no upload needed)."""
     from pathlib import Path as P
 
-    # Clean up the path: strip whitespace, quotes, and shell escape backslashes
-    path = path.strip().strip('"').strip("'")
+    # Clean up the path: strip whitespace, all quote types, shell escapes
+    path = path.strip()
+    # Strip matching or trailing quotes (handles '/path', "/path", `/path`, path')
+    for q in ('"', "'", '`'):
+        path = path.strip(q)
+    path = path.strip()
     # Remove shell-escaped spaces (e.g., /path/to/Sequencing\ Results/ → /path/to/Sequencing Results/)
     path = path.replace('\\ ', ' ')
     if path.lower().endswith('.bai'):

{bingoviewer-2.3.4 → bingoviewer-2.4.0}/bingoviewer/server/main.py

@@ -24,7 +24,7 @@ from api.genome import router as genome_router
 from api.tracks import router as tracks_router
 from api.data import router as data_router
 
-app = FastAPI(title="BiNgo Genome Viewer API", version="2.3.4")
+app = FastAPI(title="BiNgo Genome Viewer API", version="2.4.0")
 
 app.add_middleware(
     CORSMiddleware,

{bingoviewer-2.3.4 → bingoviewer-2.4.0}/bingoviewer/server/readers/bam_reader.py

@@ -5,17 +5,19 @@ CRAM is not supported by bamnostic; use BAM instead.
 """
 
 from pathlib import Path
+from typing import Optional
 
 import bamnostic as bam
 
 MAX_READS_RETURNED = 5000
+MAX_COVERAGE_READS = 500_000   # cap reads iterated for coverage computation
 READ_DETAIL_THRESHOLD = 50_000  # bp
 
 # Standard index naming conventions: file.bam.bai and file.bai
 _INDEX_SUFFIXES = (".bam.bai", ".bai")
 
 
-def _find_index(bam_path: str) -> str | None:
+def _find_index(bam_path: str) -> Optional[str]:
     """Locate a .bai index for the given BAM file.
 
     Checks both naming conventions (.bam.bai and .bai) in the same
@@ -96,8 +98,10 @@ class BamReader:
     def get_coverage(self, chrom: str, start: int, end: int, bins: int = 1000) -> list[dict]:
         """Return binned coverage by piling up fetched reads.
 
-        For performance with large BAM files, bins reads directly into
-        coverage bins instead of computing per-base depth first.
+        For large regions, splits into sub-regions (50kb chunks) to ensure
+        bamnostic's index-based fetch covers the entire span reliably.
+        Large BAM files can fail to return all reads from a single huge
+        fetch spanning millions of bases.
         """
         chrom = self._resolve_chrom(chrom)
         region_len = end - start
@@ -106,33 +110,45 @@ class BamReader:
 
         n_bins = min(bins, region_len)
         bin_size = region_len / n_bins
-        # Accumulate coverage directly into bins
-        counts = [0.0] * n_bins  # sum of base-coverage per bin
+        counts = [0.0] * n_bins
+
+        # Split large regions into chunks for reliable index traversal
+        CHUNK_SIZE = 50_000
+        total_reads = 0
+
         try:
-            for read in self._aln.fetch(chrom, start, end):
-                if read.is_unmapped:
-                    continue
-                rs = read.reference_start
-                re = read.reference_end if read.reference_end else rs + 1
-                # Clamp to region
-                rs = max(rs, start)
-                re = min(re, end)
-                if rs >= re:
-                    continue
-                # Map read span to bin range
-                bi_start = int((rs - start) / bin_size)
-                bi_end = int((re - 1 - start) / bin_size) + 1
-                bi_start = max(0, min(bi_start, n_bins - 1))
-                bi_end = max(1, min(bi_end, n_bins))
-                for bi in range(bi_start, bi_end):
-                    # Calculate overlap between read and this bin
-                    b_lo = start + bi * bin_size
-                    b_hi = start + (bi + 1) * bin_size
-                    overlap = min(re, b_hi) - max(rs, b_lo)
-                    if overlap > 0:
-                        counts[bi] += overlap / (b_hi - b_lo)
+            chunk_start = start
+            while chunk_start < end:
+                chunk_end = min(chunk_start + CHUNK_SIZE, end)
+                for read in self._aln.fetch(chrom, chunk_start, chunk_end):
+                    if read.is_unmapped:
+                        continue
+                    rs = read.reference_start
+                    re = read.reference_end if read.reference_end else rs + 1
+                    rs = max(rs, start)
+                    re = min(re, end)
+                    if rs >= re:
+                        continue
+                    bi_start = int((rs - start) / bin_size)
+                    bi_end = int((re - 1 - start) / bin_size) + 1
+                    bi_start = max(0, min(bi_start, n_bins - 1))
+                    bi_end = max(1, min(bi_end, n_bins))
+                    for bi in range(bi_start, bi_end):
+                        b_lo = start + bi * bin_size
+                        b_hi = start + (bi + 1) * bin_size
+                        overlap = min(re, b_hi) - max(rs, b_lo)
+                        if overlap > 0:
+                            counts[bi] += overlap / (b_hi - b_lo)
+                    total_reads += 1
+                    if total_reads >= MAX_COVERAGE_READS:
+                        break
+                if total_reads >= MAX_COVERAGE_READS:
+                    break
+                chunk_start = chunk_end
         except KeyError:
             return []
+        except Exception:
+            pass
 
         result = []
         for i in range(n_bins):

{bingoviewer-2.3.4 → bingoviewer-2.4.0}/pyproject.toml

@@ -4,11 +4,11 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "BiNgoViewer"
-version = "2.3.4"
+version = "2.4.0"
 description = "BiNgo Genome Viewer — a lightweight browser-based genomics viewer"
 readme = "README.md"
 license = {text = "Proprietary"}
-requires-python = ">=3.10"
+requires-python = ">=3.9"
 authors = [
     {name = "Billy M Ngo", email = "billy.ngo0108@gmail.com"},
 ]
@@ -18,6 +18,7 @@ classifiers = [
     "Intended Audience :: Science/Research",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
     "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",