Add support for specifyign a bridge adapter for more complete simulation of Dnase Hi-C.

[ShunOuchi]

Change Points

• Fixed a bug in ligation site creation When Hi-C reads were created with HindIII (A^AGCTT), the ligation site should be AAGCTAGCTT as for as I know, but in sim3C, it was AAGCTAGCTAGCTT. So I fixed it.

• Fixed an error that occurred when using the linear option Errors sometimes occur when using the linear option. So I fixed it.

  

• Set initial value of efficiency when -m dnase option is used The initial value of efficiency was not specified when using -m dnase option, so it was set.

• Fixed a bug in which read orientation was fixed when creating Hi-C reads In sim3C, the orientation of the reads was fixed as shown in the figure below. But as for as I know, the orientation of the Hi-C reads is generally random. So I fixed it.

  

• Added --bridge-adapter option Added the function to insert a bridge adapter sequence when using the -m dnase option.

• Added --sam option Added the function to output SAM format files.

[cerebis]

Dear @ShunOuchi

I appreciate this pull request. I've gotten back to maintaining sim3C and I will review what you've contributed.

[cerebis]

I am still interested in better implementing Dnase Hi-C, so I am reopening this PR