This was an oversight affecting v2.22+. The latest minimap2 ranks hits and
estimates mapping quality with an adjusted alignment score (see the minimap2
update paper). This score however is not calculated when there is only one hit.
As a result, the ms:i tag varies depends on other sequences in the reference
genome, which is confusing. This change lets minimap2 to output the unadjusted
score at ms:i. At present, the adjusted score is not outputted.
Resolves#1146
* a new option --secondary-seq to output SEQ field for secondary alignments
* comments removed
* Fixed a conflict in #687
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Co-authored-by: Heng Li <lh3@me.com>
Give the CIGAR constants names to clarify the code. So that ksw2.h
remains self-contained, define KSW_* versions of the CIGAR operators
it needs for use within ksw2.h. Other code should in general use the
full set of MM_CIGAR_* constants in minimap.h.
Define MM_CIGAR_STR to the full string of CIGAR operators (including
the 'B' operator as well) and use it throughout the C code.
It would be possible to use it from the Cython code too, but it's easier
to keep that as a Cython string literal to avoid adding extra runtime
code to handle locale conversion.
this_rid/this_pos will be copied from r_prev(=r_next)'s values when this
read is unmapped (i.e., r is NULL). In this case, we can write RNEXT as
'=' but should not calculate TLEN from these placeholder values.
Similarly when the mate is unmapped (i.e., r_next is NULL).
Fixes#365.
When a chain is split during base-level alignment, its chaining score is
reduced. However, the chaining score of its suboptimal chain remains the same.
This leads to underestimated mapping quality.
