Fix #376 - CRISPRessoPooled chunking

When running CRISPressoPooled with > 10000000 reads aligned, if there are reads overlapping the chunk boundary, instead of increasing the end with 500 bases, it takes the last position of chromosome as end position. This fixes the bug.
pinellolab · Feb 13, 2024 · 2b16392 · 2b16392
1 parent 31c65df
commit 2b16392
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/CRISPResso2/CRISPRessoPooledCORE.py b/CRISPResso2/CRISPRessoPooledCORE.py
@@ -1168,7 +1168,7 @@ def rreplace(s, old, new):
                                 n_reads_at_end = get_n_aligned_bam_region(bam_filename_genome, chr_str, curr_end-5, curr_end+5)
                                 while n_reads_at_end > 0:
                                     curr_end += 500  # look for another place with no reads
-                                    if curr_end >= curr_pos:
+                                    if curr_end >= chr_len:
                                         curr_end = chr_len
                                         break
                                     n_reads_at_end = get_n_aligned_bam_region(bam_filename_genome, chr_str, curr_end-5, curr_end+5)