From 7b4e839c96e4dfddc8f808c7d9d9100dc449e66c Mon Sep 17 00:00:00 2001
From: seina001 <seinarsson@ufl.edu>
Date: Wed, 20 Mar 2024 15:29:07 -0400
Subject: [PATCH] Update write its sites to logger

---
 itsxpress/Dedup.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/itsxpress/Dedup.py b/itsxpress/Dedup.py
index 4560921..e7fa5d8 100644
--- a/itsxpress/Dedup.py
+++ b/itsxpress/Dedup.py
@@ -1,4 +1,5 @@
 import logging
+logger = logging.getLogger(__name__)
 import gzip
 import pyzstd as zstd
 import os
@@ -98,6 +99,8 @@ def _map_func(ziprecord):
             start, stop, tlen = itspos.get_position(repseq)
             r2start = tlen - stop
             r2end = tlen - start #calculate end of R2
+            #Log start, stop, and tlen, r2start, r2end with names and sequence ids
+            logging.info("Start: {} Stop: {} Tlen: {} R2start: {} R2end: {} for sequence ID: {}".format(start, stop, tlen, r2start, r2end, record1.id))
             try:
                 if stop > tlen:
                     record1_return = record1[start:]