From 6e795c2f90e2aea4911dbd428390007de7154564 Mon Sep 17 00:00:00 2001
From: Art Rand <art.rand@nanoporetech.com>
Date: Mon, 4 Mar 2024 16:05:54 -0800
Subject: [PATCH] [dmr] Add missing help strings to dmr pair.

---
 src/dmr/subcommands.rs | 20 ++++++++++++++++++--
 1 file changed, 18 insertions(+), 2 deletions(-)

diff --git a/src/dmr/subcommands.rs b/src/dmr/subcommands.rs
index 47eb81c..4c5642f 100644
--- a/src/dmr/subcommands.rs
+++ b/src/dmr/subcommands.rs
@@ -127,9 +127,25 @@ pub struct PairwiseDmr {
     /// coverage.
     #[arg(long, alias = "min-coverage", default_value_t = 0)]
     min_valid_coverage: u64,
-    #[arg(long, num_args = 2, conflicts_with = "regions_bed")]
+    /// Prior distribution for estimating MAP-based p-value. Should be two
+    /// arguments for alpha and beta (e.g. 1.0 1.0). See
+    /// `dmr_scoring_details.md` for additional details on how the metric
+    /// is calculated.
+    #[arg(
+        long,
+        num_args = 2,
+        conflicts_with = "regions_bed",
+        hide_short_help = true
+    )]
     prior: Option<Vec<f64>>,
-    #[arg(long, default_value_t = 0.05, conflicts_with = "regions_bed")]
+    /// Consider only effect sizes greater than this when calculating the
+    /// MAP-based p-value.
+    #[arg(
+        long,
+        default_value_t = 0.05,
+        conflicts_with = "regions_bed",
+        hide_short_help = true
+    )]
     delta: f64,
     /// Sample this many reads when estimating the max coverage thresholds.
     #[arg(