fix: Fix missing read pairs in addsv.py

adamewing · Aug 4, 2022 · 9eda74b · 9eda74b
1 parent 39f7384
commit 9eda74b
Showing 1 changed file with 1 addition and 0 deletions.
diff --git a/bin/addsv.py b/bin/addsv.py
@@ -35,6 +35,7 @@ def get_reads(bam_file, chrom, start, end, svfrac):
         pair_end = read.next_reference_start + read.query_length
         if read.is_duplicate or read.is_secondary or read.is_supplementary or \
                 read.is_unmapped or read.mate_is_unmapped or \
+                read.next_reference_name != chrom or \
                 pair_end > end or read.next_reference_start < start or \
                 read_end > end or read.reference_start < start:
             continue