Opened 7 years ago

Closed 7 years ago

#819 closed defect (fixed)

SmithWaterman::operator()(4)

Reported by: Peter Owned by: Peter
Priority: minor Milestone: yat 0.12.2
Component: documentation Version: 0.12.1
Keywords: Cc:

Description (last modified by Peter)

operator is declared as

template<typename RandomAccessIterator1, typename RandomAccessIterator2>
double operator()(RandomAccessIterator1 query_begin,
                  RandomAccessIterator1 query_end,
                  RandomAccessIterator2 reference_begin,
                  RandomAccessIterator2 reference_end,
                  double mismatch=0);

but if I call it with

sw(q.begin(), q.end(), ref.begin(), ref.end(), 3)

I get CIGAR

1066S29=1X1=1X19=2X11=1X5=1292S

which doesn't really make sense since it looks like a lot of soft-clipping and as though the clipping occurs on the ref not the query sequence. and if I call

sw(ref.begin(), ref.end(), q.begin(), q.end(), 3)

I get CIGAR

29=1X1=1X19=2X11=1X5=

which makes more sense.

Should the argument in this function be changed to better reflect functionality?

Change History (3)

comment:1 Changed 7 years ago by Peter

Description: modified (diff)

comment:2 Changed 7 years ago by Peter

Milestone: yat 0.x+yat 0.12.2
Status: newassigned
Type: enhancementdefect

comment:3 Changed 7 years ago by Peter

Resolution: fixed
Status: assignedclosed

(In [3338]) closes #819. Fixes docs.

Note: See TracTickets for help on using tickets.