From 22ffd22170aaf6e23e2217c2704e496b2b3d24a4 Mon Sep 17 00:00:00 2001
From: Jayaram Kancherla <jayaram.kancherla@gmail.com>
Date: Mon, 13 Nov 2023 08:33:06 -0800
Subject: [PATCH] fix tests for trim method

---
 setup.cfg                          |  4 ++--
 src/genomicranges/GenomicRanges.py | 20 +++++++-------------
 src/genomicranges/SeqInfo.py       |  8 ++++----
 3 files changed, 13 insertions(+), 19 deletions(-)

diff --git a/setup.cfg b/setup.cfg
index b04881b..48889b0 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -50,10 +50,10 @@ package_dir =
 install_requires =
     importlib-metadata; python_version<"3.8"
     pandas
-    biocframe>=0.3.16
+    biocframe==0.3.16
     numpy
     biocgenerics
-    biocutils
+    biocutils>=0.1.1
 
 [options.packages.find]
 where = src
diff --git a/src/genomicranges/GenomicRanges.py b/src/genomicranges/GenomicRanges.py
index 9bb672c..46a6879 100644
--- a/src/genomicranges/GenomicRanges.py
+++ b/src/genomicranges/GenomicRanges.py
@@ -1,19 +1,10 @@
 import math
 import random
 from collections import OrderedDict
-from typing import (
-    Any,
-    Callable,
-    Dict,
-    List,
-    Literal,
-    Optional,
-    Union,
-)
+from typing import Any, Callable, Dict, List, Literal, Optional, Sequence, Union
 from warnings import warn
 
 from biocframe import BiocFrame
-from biocframe.types import SlicerArgTypes
 from biocgenerics.colnames import colnames, set_colnames
 from biocgenerics.combine import combine
 from biocgenerics.combine_cols import combine_cols
@@ -477,7 +468,9 @@ def __repr__(self) -> str:
         return capture.get()
 
     # for documentation, otherwise serves no real use.
-    def __getitem__(self, args: SlicerArgTypes) -> Union["GenomicRanges", dict, list]:
+    def __getitem__(
+        self, args: Union[int, str, Sequence, tuple]
+    ) -> Union["GenomicRanges", dict, list]:
         """Subset the object.
 
         This operation returns a new object with the same type as the caller.
@@ -904,10 +897,11 @@ def trim(self) -> "GenomicRanges":
         for idx in range(len(all_chrs)):
             keep = True
             t_chr = all_chrs[idx]
+            s_idx = seqinfos.seqnames.index(t_chr)
             if (
                 is_circular is not None
-                and is_circular[t_chr] is False
-                and all_ends[idx] > seqlengths[t_chr]
+                and is_circular[s_idx] is False
+                and all_ends[idx] > seqlengths[s_idx]
             ):
                 keep = False
 
diff --git a/src/genomicranges/SeqInfo.py b/src/genomicranges/SeqInfo.py
index 7e151fc..ac169bd 100644
--- a/src/genomicranges/SeqInfo.py
+++ b/src/genomicranges/SeqInfo.py
@@ -1,7 +1,7 @@
-from typing import Dict, List, Optional, Union, Sequence
-import biocutils as bu
+from typing import Dict, List, Optional, Sequence, Union
 from warnings import warn
 
+import biocutils as bu
 
 __author__ = "jkanche"
 __copyright__ = "jkanche"
@@ -112,8 +112,8 @@ def _validate_seqlengths(self):
             raise ValueError("'seqlengths' should be a list of integers")
         if n != len(self._seqlengths):
             raise ValueError("'seqnames' and 'seqlengths' should have the same length")
-        for l in self._seqlengths:
-            if l is not None and l < 0:
+        for sl in self._seqlengths:
+            if sl is not None and sl < 0:
                 raise ValueError("all entries of 'seqlengths' should be non-negative")
 
     def _validate_is_circular(self):