continue cleaning up breakpoint creation + interval methods

README.md

@@ -236,3 +236,11 @@ chr7	55610095	56049369	+	1	True	82.346163
 chr7	54763282	56049369	+	2	False	2.843655
 ```
 
+
+## FAQs
+- `call_cnvs.sh` didn't produce segmented CN calls in a .cns file?
+   - `cnvkit.py batch` contains multiple steps detailed in their 
+   [documentation](https://cnvkit.readthedocs.io/en/stable/pipeline.html). The 
+   errors from a particular stage don't always percolate up when running the
+   complete pipeline via `batch`, so try running each stage separately to 
+   pinpoint the root cause.

coral/breakpoint/breakpoint_graph.py

@@ -28,7 +28,9 @@
 class BreakpointGraph:
     """A container object for the breakpoint graphs."""
 
-    amplicon_intervals: list[datatypes.Interval] = field(default_factory=list)
+    amplicon_intervals: list[datatypes.AmpliconInterval] = field(
+        default_factory=list
+    )
     sequence_edges: list[list[Any]] = field(default_factory=list)
     concordant_edges: list[list[Any]] = field(default_factory=list)
     discordant_edges: list[list[Any]] = field(default_factory=list)

coral/breakpoint/breakpoint_types.py

@@ -3,57 +3,62 @@
 from __future__ import annotations
 
 import io
+from collections import defaultdict
 from dataclasses import dataclass
 from typing import Any, Dict, List
 
 import intervaltree
 import numpy as np
 
-from coral.types import CnsInterval
+from coral.datatypes import CNSInterval, CNSIntervalTree
 
 
 @dataclass
 class CNSSegData:
     """Container class for mapping CN (copy number) per chromosome segment, as parsed from a .cns or .bed file."""
 
-    tree: intervaltree.IntervalTree  # IntervalTree mapping chromosome segments to their (per-chromosome) index in input file
-    intervals: List[
-        CnsInterval
-    ]  # Raw list of all chromosome intervals given, of the form (chromosome, start_idx, end_idx)
-    intervals_by_chr: Dict[
-        str, List[List[int]]
-    ]  # List of chromosome intervals with their respective CNs, grouped by chromosome number
+    tree: Dict[
+        str, CNSIntervalTree
+    ]  # IntervalTree mapping chromosome segments to their (per-chromosome) index in input file
+    # Raw list of all chromosome intervals given, of the form
+    # (chromosome, start_idx, end_idx)
+    intervals: List[CNSInterval]
+    # List of chromosome intervals with their respective CNs,
+    # grouped by chromosome number
+    intervals_by_chr: Dict[str, List[CNSInterval]]
     log2_cn: List[float]  # Log2 of CN for each chromosome segment
 
     @classmethod
     def from_file(cls, file: io.TextIOWrapper) -> CNSSegData:
         """Parse CN interval data from a .cns or .bed file."""
         tree, log2_cns = {}, []
         intervals = []
-        intervals_by_chr: Dict[str, List[List[Any]]] = {}
+        intervals_by_chr: Dict[str, List[CNSInterval]] = defaultdict(list)
         is_cns = file.name.endswith(".cns")
 
         idx = 0
         for line in file:
             fields = line.strip().split()
-            if not fields or fields[0] == "chromosome" or line.startswith("#"):  # Skip potential header row
+            if (
+                not fields or fields[0] == "chromosome" or line.startswith("#")
+            ):  # Skip potential header row
                 continue
             chr_tag, start, end = fields[0], int(fields[1]), int(fields[2])
-            intervals.append([chr_tag, start, end - 1])
-            if chr_tag not in tree:
-                tree[chr_tag] = intervaltree.IntervalTree()
-                intervals_by_chr[chr_tag] = []
-                idx = 0
-            tree[chr_tag][start:end] = idx
-            idx += 1
 
             # Calc log2 CN for .cns
             log2_cn = (
                 float(fields[4]) if is_cns else np.log2(float(fields[3]) / 2.0)
             )
             raw_cn = 2 * (2**log2_cn) if is_cns else float(fields[3])
-
             log2_cns.append(log2_cn)
-            intervals_by_chr[chr_tag].append([chr_tag, start, end - 1, raw_cn])
+            cns_interval = CNSInterval(chr_tag, start, end - 1, raw_cn)
+
+            intervals.append(cns_interval)
+            intervals_by_chr[chr_tag].append(cns_interval)
+            if chr_tag not in tree:
+                tree[chr_tag] = CNSIntervalTree()
+                idx = 0
+            tree[chr_tag][start:end] = idx
+            idx += 1
 
         return cls(tree, intervals, intervals_by_chr, log2_cns)