avoid direct float comparison

Author: xinehc

src/melon/melon.py

@@ -2,6 +2,7 @@
 import json
 import numpy as np
 
+from math import isclose
 from collections import defaultdict
 from scipy.sparse import csr_matrix
 from .utils import *
@@ -199,8 +200,8 @@ def parse_minimap(self):
             alignment = alignments.pop()
             if (
                 max(alignment[2] / 0.995, alignment[2] + 50) > max_scores[alignment[0]]['AS'] or
-                alignment[3] ==  max_scores[alignment[0]]['DE'] or
-                alignment[4] ==  max_scores[alignment[0]]['ID']
+                isclose(alignment[3], max_scores[alignment[0]]['DE']) or
+                isclose(alignment[4], max_scores[alignment[0]]['ID'])
             ):
                 if (alignment[0], alignment[-1]) not in duplicates:
                     self.alignments.append(alignment)
@@ -247,10 +248,7 @@ def run_em(self, max_iterations=1000, epsilon=1e-10):
             np.copyto(p_mappings_hist, p_mappings)
 
         ## return assignments
-        assignments = []
-        for p_read in p_reads.tocsr():
-            p_read = p_read.toarray().squeeze()
-            assignments.append(np.where(p_read == p_read.max())[0].tolist())
+        assignments = [[index] for index in np.argmax(p_reads.toarray(), axis=1)]
 
         ties = defaultdict(set)
         for qseqid, lineage in enumerate(assignments):