From 702fd2538522df80ea3b76a811260f06a4a0e3e1 Mon Sep 17 00:00:00 2001
From: Veronique Legrand <vlegrand@pasteur.fr>
Date: Tue, 25 Mar 2025 16:23:24 +0100
Subject: [PATCH] added trace to get the number of lines in huge gzipped file
---
phagetermvirome/readsCoverage_res.py | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/phagetermvirome/readsCoverage_res.py b/phagetermvirome/readsCoverage_res.py
index dfea8d0..bc3d3c5 100644
--- a/phagetermvirome/readsCoverage_res.py
+++ b/phagetermvirome/readsCoverage_res.py
@@ -283,8 +283,9 @@ class RCCheckpoint_handler:
host_whole_coverage,list_hybrid,insert,paired_mismatch,reads_tested,read_match):
cur_t = time.perf_counter_ns()
elapsed_t = cur_t - self.start_t
- #convert elapsed_t tp to seconds
- elaspsed_t=elapsed_t * 0.000000001
+ #convert elapsed_t tp to seconds; then minutes
+ elapsed_t=elapsed_t * 0.000000001
+ elapsed_t=elapsed_t/60
if (self.test_mode==True or (self.chk_freq!=0 and (elapsed_t % self.chk_freq == 0))): # time to create checkpoint.
chkp=RCCheckpoint(count_line,core_id,idx_seq,termini_coverage,whole_coverage,paired_whole_coverage,\
phage_hybrid_coverage, host_hybrid_coverage, \
--
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