Factor out sort_concordance_indexes into overlap_stitcher

micall/tests/test_contig_stitcher.py

@@ -17,10 +17,10 @@
     stitch_consensus,
     calculate_concordance,
     align_all_to_reference,
-    disambiguate_concordance,
     lstrip,
     rstrip,
 )
+from micall.utils.overlap_stitcher import disambiguate_concordance
 from micall.core.plot_contigs import plot_stitcher_coverage
 from micall.tests.utils import mock_align_consensus, MockAlignment, fixed_random_seed
 from micall.tests.test_fasta_to_csv import check_hcv_db, DEFAULT_DATABASE  # activates the fixture

micall/utils/overlap_stitcher.py

@@ -1,5 +1,6 @@
 from fractions import Fraction
 from typing import Sequence, Iterator, Tuple
+from operator import itemgetter
 from gotoh import align_it
 
 
@@ -76,4 +77,9 @@ def disambiguate_concordance(concordance: Sequence[Fraction],
         yield x, global_rank
 
 
-# def get_max_
+def sort_concordance_indexes(concordance: Sequence[Fraction]) -> Sequence[int]:
+    concordance_d = disambiguate_concordance(concordance)
+    return tuple(i for i, v in sorted(enumerate(concordance_d),
+                                      key=itemgetter(1),
+                                      reverse=True,
+                                      ))

micall/utils/referencefull_contig_stitcher.py

@@ -10,15 +10,14 @@
 from Bio import Seq
 import logging
 from fractions import Fraction
-from operator import itemgetter
 from aligntools import CigarHit, connect_nonoverlapping_cigar_hits, drop_overlapping_cigar_hits, CigarActions
 
 from micall.core.project_config import ProjectConfig
 from micall.core.plot_contigs import plot_stitcher_coverage
 from micall.utils.contig_stitcher_context import context, StitcherContext
 from micall.utils.contig_stitcher_contigs import GenotypedContig, AlignedContig
 from micall.utils.consensus_aligner import align_consensus
-from micall.utils.overlap_stitcher import align_queries, calculate_concordance, disambiguate_concordance
+from micall.utils.overlap_stitcher import align_queries, calculate_concordance, sort_concordance_indexes
 import micall.utils.contig_stitcher_events as events
 
 
@@ -281,11 +280,7 @@ def find_overlapping_contig(self: AlignedContig, aligned_contigs):
 def concordance_to_cut_points(left_overlap, right_overlap, aligned_left, aligned_right, concordance):
     """ Determine optimal cut points for stitching based on sequence concordance in the overlap region. """
 
-    concordance_d = list(disambiguate_concordance(concordance))
-    sorted_concordance_indexes = [i for i, v in sorted(enumerate(concordance_d),
-                                                       key=itemgetter(1),
-                                                       reverse=True,
-                                                       )]
+    sorted_concordance_indexes = sort_concordance_indexes(concordance)
 
     def remove_dashes(s: str):
         return s.replace('-', '')