From 0d4454df102cd40623bce3d216aa2a77d88d8fad Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Nahuel=20Unai=20Rosell=C3=B3=20Beneitez?=
 <31628502+Icemole@users.noreply.github.com>
Date: Wed, 4 Sep 2024 10:31:33 +0200
Subject: [PATCH] PlotAlignmentsJob: add to all list, fixes (#541)

---
 mm/alignment.py | 16 +++++++++++-----
 1 file changed, 11 insertions(+), 5 deletions(-)

diff --git a/mm/alignment.py b/mm/alignment.py
index 2e404ae9..60d2a2a3 100644
--- a/mm/alignment.py
+++ b/mm/alignment.py
@@ -1,4 +1,10 @@
-__all__ = ["AlignmentJob", "DumpAlignmentJob", "AMScoresFromAlignmentLogJob", "ComputeTimeStampErrorJob"]
+__all__ = [
+    "AlignmentJob",
+    "DumpAlignmentJob",
+    "PlotAlignmentJob",
+    "AMScoresFromAlignmentLogJob",
+    "ComputeTimeStampErrorJob",
+]
 
 import logging
 import math
@@ -477,16 +483,16 @@ def plot(self):
 
         # Plot the data.
         matplotlib.use("Agg")
-        clip_low = max(self.clip_low, np.percentile(self.clip_percentile_low), min_value)
-        clip_high = min(self.clip_high, np.percentile(self.clip_percentile_high), max_value)
+        clip_low = max(self.clip_low, np.percentile(np_alignment_scores, self.clip_percentile_low), min_value)
+        clip_high = min(self.clip_high, np.percentile(np_alignment_scores, self.clip_percentile_high), max_value)
         np.clip(np_alignment_scores, clip_low, clip_high, out=np_alignment_scores)
         plt.hist(np_alignment_scores, bins=self.num_bins)
         plt.xlabel("Average Maximum-Likelihood Score")
         plt.ylabel("Number of Segments")
         plt.title("Histogram of Alignment Scores")
         plt.gca().set_xlim(left=self.zoom_x_min, right=self.zoom_x_max)
-        plt.gca().set_ylim(left=self.zoom_y_min, right=self.zoom_y_max)
-        plt.savefig(fname=self.out_plot_avg.get_path())
+        plt.gca().set_ylim(bottom=self.zoom_y_min, top=self.zoom_y_max)
+        plt.savefig(fname=self.out_plot.get_path())
 
 
 class AMScoresFromAlignmentLogJob(Job):