Contig stitcher: ensure match_fraction value for every contig

It is required by remap, so we have to provide something to it.
However, it is not clear how to recalculate the value for subparts
of initial contigs since it is initially set by BLAST.

The easiest would be to rerun BLAST on final contigs,
but that also seems wasteful.

Current solution simply copies the match_fraction from parent
of a subpart, or takes min of two "parents" for contigs
that are munged together.

micall/core/contig_stitcher.py

@@ -23,7 +23,7 @@ class Contig:
 class GenotypedContig(Contig):
     ref_name: str
     ref_seq: Optional[str]          # None in cases where the reference organism is unknown.
-    match_fraction: Optional[float] # Approximated overall concordance between `seq` and `ref_seq`.
+    match_fraction: float           # Approximated overall concordance between `seq` and `ref_seq`. It is calculated by BLAST as qcovhsp/100, where qcovhsp means Query Coverage Per HSP.
 
     def cut_query(self, cut_point: float) -> Tuple['GenotypedContig', 'GenotypedContig']:
         """
@@ -32,16 +32,17 @@ def cut_query(self, cut_point: float) -> Tuple['GenotypedContig', 'GenotypedCont
         """
 
         cut_point = max(0, cut_point)
+        match_fraction = self.match_fraction
         left = GenotypedContig(name=f'left({self.name})',
                                seq=self.seq[:ceil(cut_point)],
                                ref_seq=self.ref_seq,
                                ref_name=self.ref_name,
-                               match_fraction=None)
+                               match_fraction=match_fraction)
         right = GenotypedContig(name=f'right({self.name})',
                                 seq=self.seq[ceil(cut_point):],
                                 ref_seq=self.ref_seq,
                                 ref_name=self.ref_name,
-                                match_fraction=None)
+                                match_fraction=match_fraction)
 
         return (left, right)
 
@@ -167,11 +168,12 @@ def rstrip_query(self):
     @staticmethod
     def munge(left: AlignedContig, right: AlignedContig) -> AlignedContig:
         query_seq = left.rstrip_query().seq + right.lstrip_query().seq
+        match_fraction = min(left.match_fraction, right.match_fraction)
         query = GenotypedContig(seq=query_seq,
                                 name=f'{left.name}+{right.name}',
                                 ref_name=left.ref_name,
                                 ref_seq=left.ref_seq,
-                                match_fraction=None)
+                                match_fraction=match_fraction)
 
         left_alignment = left.alignment
         right_alignment = \
@@ -279,9 +281,10 @@ def stitch_2_contigs(left, right):
     overlap_seq = ''.join(c for c in aligned_left_part + aligned_right_part if c != '-')
 
     # Return something that can be fed back into the loop.
+    match_fraction = min(left.match_fraction, right.match_fraction)
     overlap_query = GenotypedContig(name=f'overlap({left.name},{right.name})',
                                     seq=overlap_seq, ref_name=left.ref_name,
-                                    ref_seq=left.ref_seq, match_fraction=None)
+                                    ref_seq=left.ref_seq, match_fraction=match_fraction)
     overlap_contig = SyntheticContig(overlap_query,
                                      r_st=left_overlap.alignment.r_st,
                                      r_ei=right_overlap.alignment.r_ei)