From 56ee2bd562788dad0dc8516d0e3db90ffa916320 Mon Sep 17 00:00:00 2001
From: Addimator <44083468+Addimator@users.noreply.github.com>
Date: Fri, 10 May 2024 13:38:50 +0200
Subject: [PATCH] fix: in bam record buffer, change the start of the window to
 the first added item in last iteration (#430)
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* Change the start of the window to the first added item in last iteration

* Change linting

* Pay attention when start_pos is None

* Change location of start_pos update

* Remove debug infos

* fmt

* Change to make rust clippy happy

---------

Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>
---
 src/bam/buffer.rs | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/bam/buffer.rs b/src/bam/buffer.rs
index 07bd17d35..2bf41d589 100644
--- a/src/bam/buffer.rs
+++ b/src/bam/buffer.rs
@@ -11,7 +11,6 @@ use std::str;
 use crate::bam;
 use crate::bam::Read;
 use crate::errors::{Error, Result};
-
 /// A buffer for BAM records. This allows access regions in a sorted BAM file while iterating
 /// over it in a single pass.
 /// The buffer is implemented as a ringbuffer, such that extension or movement to the right has
@@ -25,6 +24,7 @@ pub struct RecordBuffer {
     cache_cigar: bool,
     min_refetch_distance: u64,
     buffer_record: Rc<bam::Record>,
+    start_pos: Option<u64>,
 }
 
 unsafe impl Sync for RecordBuffer {}
@@ -45,6 +45,7 @@ impl RecordBuffer {
             cache_cigar,
             min_refetch_distance: 1,
             buffer_record: Rc::new(bam::Record::new()),
+            start_pos: Some(0),
         }
     }
 
@@ -89,7 +90,7 @@ impl RecordBuffer {
             if self.inner.is_empty()
                 || window_start.saturating_sub(self.end().unwrap()) >= self.min_refetch_distance
                 || self.tid().unwrap() != tid as i32
-                || self.start().unwrap() > window_start
+                || self.start().unwrap() > self.start_pos.unwrap()
             {
                 let end = self.reader.header.target_len(tid).unwrap();
                 self.reader.fetch((tid, window_start, end))?;
@@ -145,6 +146,7 @@ impl RecordBuffer {
                     added += 1;
                 }
             }
+            self.start_pos = Some(self.start().unwrap_or(window_start));
 
             Ok((added, deleted))
         } else {