Increase the pair window by an alignment length

[ekg]

Trying to recover some lost accuracy from the performance refresh.

[ekg]

10M reads with the version here:

human_sim.10M.3ed9402.ROC.1.pdf

human_sim.3ed9402.QQ.1.pdf

Runtimes:

bwa mem paired
[main] Version: 0.7.15-r1142-dirty
[main] CMD: bwa mem -t 32 hs37d5/hs37d5.fa human.10M/sim_1.fq.gz human.10M/sim_2.fq.gz
[main] Real time: 460.096 sec; CPU: 12691.821 sec
  10M 0:07:40 [21.7k/s]
real    7m55.307s
user    210m53.962s
sys     6m9.095s

bwa mem single
[main] Version: 0.7.15-r1142-dirty
[main] CMD: bwa mem -t 32 hs37d5/hs37d5.fa /dev/fd/63
[main] Real time: 561.963 sec; CPU: 12223.657 sec
  10M 0:09:21 [17.8k/s]
real    9m37.149s
user    201m5.182s
sys     7m20.999s

vg ref paired mapping
  10M 1:11:51 [2.32k/s] 
real    72m6.630s
user    2252m9.570s
sys     9m3.661s

vg ref single mapping
  10M 1:17:06 [2.16k/s]
real    77m21.681s
user    2424m24.365s
sys     9m44.287s

vg pan paired mappping
  10M 1:00:54 [2.74k/s]
real    61m10.115s
user    1859m7.811s
sys     10m6.860s

vg pan single mappping
  10M 0:54:36 [3.05k/s]
real    54m51.761s
user    1637m27.120s
sys     9m12.025s