From 8a12cd63d5f426353c3738c8591ac6a7b98860bf Mon Sep 17 00:00:00 2001
From: Donald Campbell <125581724+donaldcampbelljr@users.noreply.github.com>
Date: Thu, 12 Dec 2024 16:34:13 -0500
Subject: [PATCH] more work towards #56, skip count for start less than current
 position

---
 gtars/src/uniwig/counting.rs | 29 +++++++++++++----------------
 1 file changed, 13 insertions(+), 16 deletions(-)

diff --git a/gtars/src/uniwig/counting.rs b/gtars/src/uniwig/counting.rs
index e97b74c..03bb1eb 100644
--- a/gtars/src/uniwig/counting.rs
+++ b/gtars/src/uniwig/counting.rs
@@ -1328,34 +1328,31 @@ pub fn variable_shifted_bam_to_bw( records: &mut Box<Query<noodles::bgzf::reader
         adjusted_start_site = shifted_pos - smoothsize;
 
 
-        count += 1;
-
         if adjusted_start_site < 0 {
             adjusted_start_site = 0;
         }
 
         let new_end_site = adjusted_start_site + 1 + smoothsize * 2;
-        println!("adjusted start site for new coord: {}", adjusted_start_site);
-        println!("new endsite for new coord: {}", new_end_site);
-
-        if new_end_site < current_end_site {
-            collected_end_sites.insert(0, current_end_site); // put the current end site back into the queue
-            current_end_site = new_end_site;
-        } else
-        {
+        //println!("adjusted start site for new coord: {}", adjusted_start_site);
+        //println!("new endsite for new coord: {}", new_end_site);
+
+        if new_end_site < current_end_site || coordinate_position > adjusted_start_site{
+            continue;
+        } else{
             collected_end_sites.push(new_end_site);
         }
 
-        println!("here is all endsites: {:?}", collected_end_sites);
+        count += 1;
+        //println!("here is all endsites: {:?}", collected_end_sites);
 
         if adjusted_start_site == prev_coordinate_value {
             continue;
         }
 
         while coordinate_position < adjusted_start_site {
-            println!("coordinate_position< adjusted_start_site: {} < {} . here is current endsite: {} ", coordinate_position, adjusted_start_site, current_end_site);
+            //println!("coordinate_position< adjusted_start_site: {} < {} . here is current endsite: {} ", coordinate_position, adjusted_start_site, current_end_site);
             while current_end_site == coordinate_position {
-                println!("current_end_site == coordinate_position {} = {} adjusted start site: {}", current_end_site, coordinate_position, adjusted_start_site);
+                //println!("current_end_site == coordinate_position {} = {} adjusted start site: {}", current_end_site, coordinate_position, adjusted_start_site);
                 count = count - 1;
 
                 //prev_end_site = current_end_site;
@@ -1368,7 +1365,7 @@ pub fn variable_shifted_bam_to_bw( records: &mut Box<Query<noodles::bgzf::reader
                     current_end_site = 0;
                 } else {
                     current_end_site = collected_end_sites.remove(0);
-                    println!("new endsite deom deque: {}", current_end_site);
+                    //println!("new endsite deom deque: {}", current_end_site);
                 }
             }
 
@@ -1530,8 +1527,8 @@ pub fn get_shifted_pos(flags: &Flags, start_site:i32, end_site:i32) -> i32 {
         }
     }
 
-    println!("Here is read.reference_start {} and read.reference_end {}", start_site, end_site);
-    println!("here is shifted_pos -> {shifted_pos}");
+    //println!("Here is read.reference_start {} and read.reference_end {}", start_site, end_site);
+    //println!("here is shifted_pos -> {shifted_pos}");
 
     shifted_pos
 }
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