From 56ca8ce910e7d3e669e681aaa17f01e1ef46f839 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 18 Dec 2023 10:50:05 +0100
Subject: [PATCH] read.rs: fix bug leading to empty bam
---
src/read.rs | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/src/read.rs b/src/read.rs
index e6a4f92..75c3cb7 100644
--- a/src/read.rs
+++ b/src/read.rs
@@ -118,7 +118,7 @@ impl Fragments {
pub fn next_chr(&mut self) {
loop {
self.get_chr();
- if !self.check_name() {
+ if self.check_name() {
break;
}
}
@@ -141,7 +141,7 @@ impl Fragments {
while self.chr_id < chr_id {
self.next_chr();
}
- if chr_pos > self.chr_seq.len() as u32 - self.fragment_len {
+ if chr_pos > self.chr_seq.len() as u32 {
panic!(
"Fragments::get_single() pos {} not present in chromosome {}:{} of size {}",
chr_pos,
@@ -171,7 +171,7 @@ impl Fragments {
while self.chr_id < chr_id {
self.next_chr();
}
- if chr_pos >= self.chr_seq.len() as u32 - self.fragment_len {
+ if chr_pos >= self.chr_seq.len() as u32 {
panic!(
"Fragments::get() pos {} not present in chromosome {} of size {}",
chr_pos,
@@ -306,7 +306,7 @@ impl Read {
/// # Return
/// String
fn build_name(read_number: u64, paired: bool, first: bool) -> String {
- let mut read_name = String::from("bigwig2bam:0:0:0:");
+ let mut read_name = String::from("bigwig2bam:0:1:3:");
read_name.push_str(&read_number.to_string());
if paired {
if first {
--
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