From d99ea892fea85b6dd0482c6ec97c61475b06b206 Mon Sep 17 00:00:00 2001
From: alexsweeten <alex.sweeten@gmail.com>
Date: Thu, 13 Jun 2024 11:27:10 -0400
Subject: [PATCH 1/2] Bugfix for comparative mode of different sizes

---
 src/moddotplot/moddotplot.py   | 26 +++++++++++++++++++-------
 src/moddotplot/static_plots.py |  3 ---
 2 files changed, 19 insertions(+), 10 deletions(-)

diff --git a/src/moddotplot/moddotplot.py b/src/moddotplot/moddotplot.py
index 91a9d11..dfeb282 100644
--- a/src/moddotplot/moddotplot.py
+++ b/src/moddotplot/moddotplot.py
@@ -528,7 +528,9 @@ def main():
 
     # Throw error if compare only selected with one sequence.
     if len(k_list) < 2 and args.compare_only:
-        print(f"Error: Can't create a comparative plot with only one sequence")
+        print(
+            f"Error: Can't create a comparative plot with only one sequence. Please re-run without --compare-only."
+        )
         sys.exit(2)
 
     # -----------LAUNCH INTERACTIVE MODE-----------
@@ -910,7 +912,7 @@ def main():
                         axes_labels=args.axes_ticks,
                     )
 
-        # -----------COMPUTE COMAPRATIVE PLOTS-----------
+        # -----------COMPUTE COMPARATIVE PLOTS-----------
         # TODO: Optimize computations so that largest sequence doesn't need to be redone all the time
         if (args.compare or args.compare_only) and len(sequences) > 1:
             # Set window size to args.window. Otherwise, set it to n/resolution
@@ -937,16 +939,26 @@ def main():
                     smaller_seq = sequences[j][1]
                     larger_length = len(larger_seq)
                     smaller_length = len(smaller_seq)
+                    larger_seq_name = sequences[i][0]
+                    smaller_seq_name = sequences[j][0]
+                    # Houston we have a problem
+                    if larger_length < smaller_length:
+                        smaller_seq = sequences[i][1]
+                        larger_seq = sequences[j][1]
+                        larger_length = len(larger_seq)
+                        smaller_length = len(smaller_seq)
+                        larger_seq_name = sequences[j][0]
+                        smaller_seq_name = sequences[i][0]
                     print(
-                        f"Computing pairwise identity matrix for {sequences[i][0]} and {sequences[j][0]}... \n"
+                        f"Computing pairwise identity matrix for {larger_seq_name} and {smaller_seq_name}... \n"
                     )
                     # TODO: Logging here
                     # print(f"\tSparsity value s: {seq_sparsity}\n")
                     print(
-                        f"\tSequence length {sequences[i][0]}: {larger_length + args.kmer - 1}\n"
+                        f"\tSequence length {larger_seq_name}: {larger_length + args.kmer - 1}\n"
                     )
                     print(
-                        f"\tSequence length {sequences[j][0]}: {smaller_length + args.kmer - 1}\n"
+                        f"\tSequence length {smaller_seq_name}: {smaller_length + args.kmer - 1}\n"
                     )
                     print(f"\tWindow size w: {win}\n")
                     print(f"\tModimizer sketch size: {expectation}\n")
@@ -955,8 +967,8 @@ def main():
                     pair_mat = createPairwiseMatrix(
                         larger_length,
                         smaller_length,
-                        sequences[i][1],
-                        sequences[j][1],
+                        larger_seq,
+                        smaller_seq,
                         win,
                         seq_sparsity,
                         args.delta,
diff --git a/src/moddotplot/static_plots.py b/src/moddotplot/static_plots.py
index 55ab85a..b71018d 100644
--- a/src/moddotplot/static_plots.py
+++ b/src/moddotplot/static_plots.py
@@ -175,8 +175,6 @@ def make_dot(sdf, title_name, palette, palette_orientation, colors, breaks, xlim
         breaks = [float(number) for number in breaks]
     if not xlim:
         xlim = 0
-    else:
-        breaks = [float(number) for number in breaks]
     hexcodes = []
     new_hexcodes = []
     if palette in DIVERGING_PALETTES:
@@ -403,7 +401,6 @@ def create_plots(
         sdf, palette, palette_orientation, custom_colors, custom_breakpoints
     )
 
-    print(xlim)
     if is_pairwise:
         heatmap = make_dot(
             sdf,

From 069cc23f73178185f20f7da3b7854898be8db408 Mon Sep 17 00:00:00 2001
From: alexsweeten <alex.sweeten@gmail.com>
Date: Thu, 13 Jun 2024 11:28:27 -0400
Subject: [PATCH 2/2] Bump version, remove numpy restriction

---
 pyproject.toml          | 4 ++--
 src/moddotplot/const.py | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 193bc8b..91a59cf 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "ModDotPlot"
-version = "0.8.3"
+version = "0.8.4"
 requires-python = ">= 3.7"
 dependencies = [
   "pysam",
@@ -16,7 +16,7 @@ dependencies = [
   "mmh3",
   "tk",
   "setproctitle",
-  "numpy==1.26.4"
+  "numpy"
 ]
 authors = [
   {name = "Alex Sweeten", email = "alex.sweeten@nih.gov"},
diff --git a/src/moddotplot/const.py b/src/moddotplot/const.py
index d918332..f283d4a 100644
--- a/src/moddotplot/const.py
+++ b/src/moddotplot/const.py
@@ -1,4 +1,4 @@
-VERSION = "0.8.3"
+VERSION = "0.8.4"
 COLS = [
     "#query_name",
     "query_start",