added reindex function

Author: Tina04021997

SigProfilerAssignment/decomposition.py

@@ -24,6 +24,7 @@
     SigProfilerMatrixGeneratorFunc as datadump,
 )
 from SigProfilerMatrixGenerator.scripts import CNVMatrixGenerator as scna
+from sigProfilerPlotting import sigProfilerPlotting as sigPlot
 import sigProfilerPlotting
 import os, sys
 from PyPDF2 import PdfMerger
@@ -302,6 +303,9 @@ def spa_analyze(
     mutation_type = str(genomes.shape[0])
     m = mutation_type
 
+    # Re-indexing the input matrix file by using process_input function from SigProfilePlotting
+    genomes = sigPlot.process_input(genomes, m)
+
     m_for_subgroups = ""
     if m == "96" or m == "288" or m == "1536":
         m_for_subgroups = "SBS"