Merge pull request #3 from lavenderyuuu/patch-3

Update altref.py
HKU-BAL · Apr 16, 2021 · edb5f42 · edb5f42
2 parents 9b9286b + 189cb27
commit edb5f42
Showing 1 changed file with 3 additions and 2 deletions.
diff --git a/src/altref.py b/src/altref.py
@@ -397,8 +397,9 @@ def align(self, sv_str=None):
             out_ref = self.out_ref
             fastq = self.filtered_read_fasta
             out_bam = self.out_bam
-
-        ref_size = math.ceil(1. * path.getsize(out_ref) / 1024 / 1024 / 1024 + .5)
+
+        #ref_size = math.ceil(1. * path.getsize(out_ref) / 1024 / 1024 / 1024 + .5)
+        ref_size = math.ceil((1. * path.getsize(out_ref) / 1e9 + .5) * 1.1)
         minimap2_option_split_index_for_every_N_bases = f'-I {ref_size}G' if ref_size > 4 else ''
         cmd = (
             f'{minimap2} -Y {minimap2_option_split_index_for_every_N_bases} -t {nprocs} --MD -a {out_ref} {fastq} | '