From b1f2e019dce2b44e56b5c9062c00893e41e02cf7 Mon Sep 17 00:00:00 2001
From: Adam English <ACEnglish@gmail.com>
Date: Sun, 4 Feb 2024 16:39:30 -0500
Subject: [PATCH] pylint and test files

---
 repo_utils/test_files/beds/boundary_cpx.bed       |   3 +++
 .../test_files/variants/boundary_cpx.vcf.gz       | Bin 0 -> 567 bytes
 .../test_files/variants/boundary_cpx.vcf.gz.tbi   | Bin 0 -> 132 bytes
 truvari/region_vcf_iter.py                        |   7 +++----
 4 files changed, 6 insertions(+), 4 deletions(-)
 create mode 100644 repo_utils/test_files/beds/boundary_cpx.bed
 create mode 100644 repo_utils/test_files/variants/boundary_cpx.vcf.gz
 create mode 100644 repo_utils/test_files/variants/boundary_cpx.vcf.gz.tbi

diff --git a/repo_utils/test_files/beds/boundary_cpx.bed b/repo_utils/test_files/beds/boundary_cpx.bed
new file mode 100644
index 00000000..c1af045b
--- /dev/null
+++ b/repo_utils/test_files/beds/boundary_cpx.bed
@@ -0,0 +1,3 @@
+reference	10	20
+reference	110	120
+reference2	10	20
diff --git a/repo_utils/test_files/variants/boundary_cpx.vcf.gz b/repo_utils/test_files/variants/boundary_cpx.vcf.gz
new file mode 100644
index 0000000000000000000000000000000000000000..57aba8042e31e71ebdaa0e8c849095b83f6c6d2a
GIT binary patch
literal 567
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literal 0
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diff --git a/repo_utils/test_files/variants/boundary_cpx.vcf.gz.tbi b/repo_utils/test_files/variants/boundary_cpx.vcf.gz.tbi
new file mode 100644
index 0000000000000000000000000000000000000000..83718c31d40191a3d68ab768b3438101a9ef638a
GIT binary patch
literal 132
zcmb2|=3rp}f&Xj_PR>jW=?vV3pHfni5)v2^-86WaP6b4XbaV$@4(bm2JSkXEM|p#j
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literal 0
HcmV?d00001

diff --git a/truvari/region_vcf_iter.py b/truvari/region_vcf_iter.py
index c941a875..04fa82cb 100644
--- a/truvari/region_vcf_iter.py
+++ b/truvari/region_vcf_iter.py
@@ -172,7 +172,7 @@ def region_filter(vcf, tree, inside=True):
         cur_tree = deque(sorted(cur_tree))
         try:
             cur_intv = cur_tree.popleft()
-        except IndexError as e:
+        except IndexError:
             # region-less chromosome
             continue
 
@@ -182,12 +182,12 @@ def region_filter(vcf, tree, inside=True):
             if start > cur_intv.end - 1:
                 try:
                     cur_intv = cur_tree.popleft()
-                except IndexError as e:
+                except IndexError:
                     if not inside:
                         yield entry
                         continue
                     # next chromosome
-                    break 
+                    break
 
             # well before
             if end < cur_intv.begin:
@@ -199,4 +199,3 @@ def region_filter(vcf, tree, inside=True):
             is_within = truvari.coords_within(start, end, cur_intv.begin, cur_intv.end - 1, end_within)
             if is_within == inside:
                 yield entry
-