wfmash seems much slower in -Y # mode compared to -X, although the input follows the PanSN-spec

[subwaystation]

	Command being timed: "wfmash LPA.fa.gz LPA.fa.gz -p 70 -s 500 -X"
	User time (seconds): 14.26
	System time (seconds): 0.16
	Percent of CPU this job got: 99%
	Elapsed (wall clock) time (h:mm:ss or m:ss): 0:14.49
	Average shared text size (kbytes): 0
	Average unshared data size (kbytes): 0
	Average stack size (kbytes): 0
	Average total size (kbytes): 0
	Maximum resident set size (kbytes): 149116
	Average resident set size (kbytes): 0
	Major (requiring I/O) page faults: 0
	Minor (reclaiming a frame) page faults: 8328
	Voluntary context switches: 34527
	Involuntary context switches: 44
	Swaps: 0
	File system inputs: 0
	File system outputs: 128
	Socket messages sent: 0
	Socket messages received: 0
	Signals delivered: 0
	Page size (bytes): 4096
	Exit status: 0

	Command being timed: "wfmash LPA.fa.gz LPA.fa.gz -p 70 -s 500 -Y #"
	User time (seconds): 47.30
	System time (seconds): 3.37
	Percent of CPU this job got: 103%
	Elapsed (wall clock) time (h:mm:ss or m:ss): 0:49.07
	Average shared text size (kbytes): 0
	Average unshared data size (kbytes): 0
	Average stack size (kbytes): 0
	Average total size (kbytes): 0
	Maximum resident set size (kbytes): 182840
	Average resident set size (kbytes): 0
	Major (requiring I/O) page faults: 0
	Minor (reclaiming a frame) page faults: 63761
	Voluntary context switches: 600318
	Involuntary context switches: 162
	Swaps: 0
	File system inputs: 0
	File system outputs: 2456
	Socket messages sent: 0
	Socket messages received: 0
	Signals delivered: 0
	Page size (bytes): 4096
	Exit status: 0

I would expect the exact same speed in both modes, because the input follows the PanSN-spec.

chm13#0#tig00000001	330243	21	60	61
chm1#0#tig00000003	227072	335789	60	61
HG002#0#tig00000001	329347	566667	60	61
HG002#1#tig00000005	274138	901525	60	61
HG00733#0#tig00000001	295824	1180255	60	61
HG00733#1#tig00000008	283680	1481033	60	61
HG01358#0#tig00000002	337324	1769464	60	61
HG01358#1#tig00000010	240282	2112434	60	61
HG02572#0#tig00000005	311357	2356744	60	61
HG02572#1#tig00000001	309189	2673314	60	61
NA19239#0#tig00000002	264003	2987680	60	61
NA19239#1#tig00000006	236974	3256107	60	61
NA19240#0#tig00000001	285146	3497054	60	61
NA19240#1#tig00000012	260090	3786976	60	61

I tested with the current master.
Thanks for any feedback!