From dfa4d955dddfccf0b958baa3e7edd2563c9cff28 Mon Sep 17 00:00:00 2001
From: wdecoster <decosterwouter@gmail.com>
Date: Thu, 4 Jul 2024 21:54:05 +0200
Subject: [PATCH] change warning when no (phased) reads found

---
 Cargo.toml       | 2 +-
 src/parse_bam.rs | 5 +++--
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/Cargo.toml b/Cargo.toml
index 80d873a..ca4de92 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "STRdust"
-version = "0.8.5"
+version = "0.8.6"
 edition = "2021"
 
 
diff --git a/src/parse_bam.rs b/src/parse_bam.rs
index ee46999..f558dac 100644
--- a/src/parse_bam.rs
+++ b/src/parse_bam.rs
@@ -1,3 +1,4 @@
+use log::warn;
 use rust_htslib::bam;
 use rust_htslib::bam::ext::BamRecordExtensions;
 use rust_htslib::bam::record::Aux;
@@ -78,9 +79,9 @@ pub fn get_overlapping_reads(
     if seqs.is_empty() {
         // error/warning message depends on whether we are looking for phased reads or not
         if unphased {
-            eprintln!("Cannot genotype {repeat}: no reads found");
+            warn!("Cannot genotype {repeat}: no reads found");
         } else {
-            eprintln!("Cannot genotype {repeat}: no phased reads found");
+            warn!("Cannot genotype {repeat}: no phased reads found. Use --unphased to genotype unphased reads.");
         }
         None
     } else {