From d02273f57fe1232a2d268eb2b61238afde6ae756 Mon Sep 17 00:00:00 2001
From: Matty Allan <31744230+matthewfallan@users.noreply.github.com>
Date: Fri, 18 Oct 2024 15:00:46 -0400
Subject: [PATCH 1/3] Update help text for verbose and quiet

---
 src/seismicrna/core/arg/cli.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/seismicrna/core/arg/cli.py b/src/seismicrna/core/arg/cli.py
index 93e1abb0..3552c03e 100644
--- a/src/seismicrna/core/arg/cli.py
+++ b/src/seismicrna/core/arg/cli.py
@@ -1338,13 +1338,13 @@
 opt_verbose = Option(
     ("--verbose", "-v"),
     count=True,
-    help="Log info (-v) or info and debug (-vv) messages on stdout"
+    help="Log more messages (-v, -vv, or -vvv) on stderr"
 )
 
 opt_quiet = Option(
     ("--quiet", "-q"),
     count=True,
-    help="Suppress warnings (-q) or warnings and errors (-qq) on stdout"
+    help="Log fewer messages (-q, -qq, or -qqq) on stderr"
 )
 
 opt_log = Option(

From c436f4630bcb216239dcea378a37a67170bccf77 Mon Sep 17 00:00:00 2001
From: Matty Allan <31744230+matthewfallan@users.noreply.github.com>
Date: Fri, 18 Oct 2024 15:04:55 -0400
Subject: [PATCH 2/3] Change logger.debug to logger.detail

---
 src/seismicrna/mask/write.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/seismicrna/mask/write.py b/src/seismicrna/mask/write.py
index 59f294a9..d734f3dd 100644
--- a/src/seismicrna/mask/write.py
+++ b/src/seismicrna/mask/write.py
@@ -204,8 +204,8 @@ def _filter_discontig(self, batch: SectionMutsBatch):
         """ Filter out reads with discontiguous mates. """
         if not self.mask_discontig:
             # Keep discontiguous reads.
-            logger.debug(f"{self} skipped filtering reads with "
-                         f"discontiguous mates in {batch}")
+            logger.detail(f"{self} skipped filtering reads with "
+                          f"discontiguous mates in {batch}")
             return batch
         # Find the reads with contiguous mates.
         reads = batch.read_nums[batch.contiguous]

From 55bb78fd45efd34bbe71935aad2e0eccb36ef8ef Mon Sep 17 00:00:00 2001
From: Matty Allan <31744230+matthewfallan@users.noreply.github.com>
Date: Fri, 18 Oct 2024 15:05:24 -0400
Subject: [PATCH 3/3] Bump version to 0.21.1

---
 src/seismicrna/core/version.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/seismicrna/core/version.py b/src/seismicrna/core/version.py
index 1ae6e349..19283039 100644
--- a/src/seismicrna/core/version.py
+++ b/src/seismicrna/core/version.py
@@ -1,7 +1,7 @@
 import re
 
 
-__version__ = "0.21.0"
+__version__ = "0.21.1"
 
 
 def parse_version(version: str = __version__):