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cbg-ethz · Aug 9, 2024 · b69c793 · b69c793
1 parent 279cc63
commit b69c793
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Showing 2 changed files with 3 additions and 4 deletions.
diff --git a/viloca/b2w.py b/viloca/b2w.py
@@ -354,8 +354,6 @@ def parallel_run_one_window(
         threads=1
     )
 
-    reads = open(f"reads_{idx}.fas", "w")
-
     logging.info(f"Working on window (1-based) @ {window_start+1}")
 
 #    (arr, arr_read_qualities_summary, arr_read_summary,
@@ -388,6 +386,7 @@ def parallel_run_one_window(
     else:
         end_extended_by_a_window = region_end + window_length*3
 
+    reads = open(f"reads_{idx}.fas", "w")
     for read in arr_read_summary:
         if idx == len(tiling) - 1 and read[1] > end_extended_by_a_window:
             continue

diff --git a/viloca/shotgun.py b/viloca/shotgun.py
@@ -120,7 +120,7 @@ def parse_aligned_reads(reads_file):
         # end index of the aligned read w.r.t reference (1-based indexing)
         out_reads[name][3] = int(mstop)
         out_reads[name][4] = this_m
-
+    handle.close()
     return out_reads
 
 
@@ -311,7 +311,7 @@ def win_to_run(alpha_w, seed, inference_type, n_max_haplotypes, n_mfa_starts, un
         if not os.path.isfile(output_name):
             j = min(300_000, int(cov) * 15)
             rn_list.append((winFile, j, alpha_w, seed, inference_type, n_max_haplotypes, n_mfa_starts, unique_modus, inference_convergence_threshold))
-
+    file1.close()
     del end
     del(beg, chr1)
     return rn_list