From b2633853fa76475cc1d286dd231bf46746d0a261 Mon Sep 17 00:00:00 2001
From: pdimens <pdimens@live.com>
Date: Mon, 29 Apr 2024 15:00:53 -0400
Subject: [PATCH] update text and docstrings

---
 src/harpy/__main__.py            | 8 ++++++--
 src/harpy/simulatelinkedreads.py | 2 +-
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/src/harpy/__main__.py b/src/harpy/__main__.py
index f077a2932..72cb135e6 100644
--- a/src/harpy/__main__.py
+++ b/src/harpy/__main__.py
@@ -197,9 +197,13 @@ def simulate():
     "harpy simulate":
         [
             {
-                "name": "Genomic Variants",
-                "commands": ["linkedreads", "snpindel","inversion", "cnv", "translocation"],
+                "name": "Linked Read Sequences",
+                "commands": ["linkedreads"],
             },
+            {
+                "name": "Genomic Variants",
+                "commands": ["snpindel","inversion", "cnv", "translocation"],
+            }
         ]
 }
 
diff --git a/src/harpy/simulatelinkedreads.py b/src/harpy/simulatelinkedreads.py
index 6c298ad9f..95ef2a25d 100644
--- a/src/harpy/simulatelinkedreads.py
+++ b/src/harpy/simulatelinkedreads.py
@@ -10,7 +10,7 @@
 @click.option('-i', '--distance-sd', type = click.IntRange(min = 1), default = 15, show_default=True,  help = "Standard deviation of read-pair distance")
 @click.option('-b', '--barcodes', type = click.Path(exists=True, dir_okay=False), help = "File of linked-read barcodes to add to reads")
 @click.option('-n', '--read-pairs', type = click.FloatRange(min = 0.001), default = 600, show_default=True,  help = "Number (in millions) of read pairs to simulate")
-@click.option('-l', '--molecule-length', type = click.IntRange(min = 10), default = 100, show_default=True,  help = "Mean molecule length (kbp)")
+@click.option('-l', '--molecule-length', type = click.IntRange(min = 2), default = 100, show_default=True,  help = "Mean molecule length (kbp)")
 @click.option('-p', '--partitions', type = click.IntRange(min = 1), default=1500, show_default=True,  help = "Number (in thousands) of partitions/beads to generate")
 @click.option('-m', '--molecules-per', type = click.IntRange(min = 1), default = 10, show_default=True,  help = "Average number of molecules per partition")
 @click.option('-t', '--threads', default = 4, show_default = True, type = click.IntRange(min = 1, max_open = True), help = 'Number of threads to use')