r524: reverted to bwa-mem end bonus

and reduced the cost of clipping when filtering by identity

tex/minimap2.tex

@@ -512,7 +512,11 @@ We evaluated minimap2 along with Bowtie2~\citep{Langmead:2012fk}, BWA-MEM and
 SNAP~\citep{Zaharia:2011aa}. Minimap2 is 3--4 times as fast as Bowtie2 and
 BWA-MEM, but is 1.3 times slower than SNAP. Minimap2 is more accurate on this
 simulated data set than Bowtie2 and SNAP but less accurate than BWA-MEM
-(Fig.~\ref{fig:eval}b).
+(Fig.~\ref{fig:eval}b). Closer investigation reveals that BWA-MEM achieves
+a higher accuracy partly because it tries to locally align a read in a small
+region close to its mate. If we disable this feature, BWA-MEM becomes slightly
+less accurate than minimap2. We might consider to implement a similar heuristic
+in minimap2 in future.
 
 \section{Conclusion}