// File: simonrharris[P]SKA/src/ska.cpp
// Function: mapHelp()
int mapHelp(void){
	std::cout << std::endl << "Usage:" << std::endl;
	std::cout << "ska map [options] <split kmer files>" << std::endl << std::endl;
	std::cout << "Options:" << std::endl;
	std::cout << "-a <file>\tMap all bases of kmers (Default = just map middle base)." << std::endl;
	std::cout << "-c\t\tTreat all reference contigs as circular." << std::endl;
	std::cout << "-h\t\tPrint this help." << std::endl;
	std::cout << "-f <file>\tFile of split kmer file names. These will be added to or \n\t\tused as an alternative input to the list provided on the \n\t\tcommand line." << std::endl;
	std::cout << "-k <int>\tSplit Kmer size. The kmer used for searches will be twice \n\t\tthis length, with the variable base in the middle. e.g. a \n\t\tkmer of 15 will search for 31 base matches with the middle \n\t\tbase being allowed to vary. Must be divisible by 3. \n\t\tMust be the same value used to create the kmer files. \n\t\t[Default = 15]" << std::endl;
	std::cout << "-i\t\tInclude reference sequence in alignment." << std::endl;
	std::cout << "-m\t\tMap bases to repeats rather than making them N." << std::endl;
	std::cout << "-o <file>\tOutput file prefix. [Default = mappedkmers]" << std::endl;
	std::cout << "-r <file>\tReference fasta file name. [Required]" << std::endl;
	std::cout << "-s <file>\tFile of sample names to include in the alignment." << std::endl;
	std::cout << "-v\t\tOutput variant only alignment. [Default = all sites]" << std::endl << std::endl;
	return 0;
}

// Assembly:
pushq %rbp
movq %rsp, %rbp
movq 0x258fd(%rip), %rdi     # 0x78fa8
movq 0x258de(%rip), %rsi     # 0x78f90
callq 0x6570
movq %rax, %rdi
leaq 0x733f(%rip), %rsi      # 0x5aa00
callq 0x6520
movq %rax, %rdi
movq 0x258c0(%rip), %rsi     # 0x78f90
callq 0x6570
movq 0x258cc(%rip), %rdi     # 0x78fa8
leaq 0x8c75(%rip), %rsi      # 0x5c358
callq 0x6520
movq %rax, %rdi
movq 0x2589e(%rip), %rsi     # 0x78f90
callq 0x6570
movq %rax, %rdi
movq 0x2588f(%rip), %rsi     # 0x78f90
callq 0x6570
movq 0x2589b(%rip), %rdi     # 0x78fa8
leaq 0x7745(%rip), %rsi      # 0x5ae59
callq 0x6520
movq %rax, %rdi
movq 0x2586d(%rip), %rsi     # 0x78f90
callq 0x6570
movq 0x25879(%rip), %rdi     # 0x78fa8
leaq 0x8c47(%rip), %rsi      # 0x5c37d
callq 0x6520
movq %rax, %rdi
movq 0x2584b(%rip), %rsi     # 0x78f90
callq 0x6570
movq 0x25857(%rip), %rdi     # 0x78fa8
leaq 0x8c68(%rip), %rsi      # 0x5c3c0
callq 0x6520
movq %rax, %rdi
movq 0x25829(%rip), %rsi     # 0x78f90
callq 0x6570
movq 0x25835(%rip), %rdi     # 0x78fa8
leaq 0x76e8(%rip), %rsi      # 0x5ae62
callq 0x6520
movq %rax, %rdi
movq 0x25807(%rip), %rsi     # 0x78f90
callq 0x6570
movq 0x25813(%rip), %rdi     # 0x78fa8
leaq 0x794c(%rip), %rsi      # 0x5b0e8
callq 0x6520
movq %rax, %rdi
movq 0x257e5(%rip), %rsi     # 0x78f90
callq 0x6570
movq 0x257f1(%rip), %rdi     # 0x78fa8
leaq 0x8c2f(%rip), %rsi      # 0x5c3ed
callq 0x6520
movq %rax, %rdi
movq 0x257c3(%rip), %rsi     # 0x78f90
callq 0x6570
movq 0x257cf(%rip), %rdi     # 0x78fa8
leaq 0x8d4d(%rip), %rsi      # 0x5c52d
callq 0x6520
movq %rax, %rdi
movq 0x257a1(%rip), %rsi     # 0x78f90
callq 0x6570
movq 0x257ad(%rip), %rdi     # 0x78fa8
leaq 0x8d58(%rip), %rsi      # 0x5c55a
callq 0x6520
movq %rax, %rdi
movq 0x2577f(%rip), %rsi     # 0x78f90
callq 0x6570
movq 0x2578b(%rip), %rdi     # 0x78fa8
leaq 0x8d6a(%rip), %rsi      # 0x5c58e
callq 0x6520
movq %rax, %rdi
movq 0x2575d(%rip), %rsi     # 0x78f90
callq 0x6570
movq 0x25769(%rip), %rdi     # 0x78fa8
leaq 0x8d7e(%rip), %rsi      # 0x5c5c4
callq 0x6520
movq %rax, %rdi
movq 0x2573b(%rip), %rsi     # 0x78f90
callq 0x6570
movq 0x25747(%rip), %rdi     # 0x78fa8
leaq 0x7a05(%rip), %rsi      # 0x5b26d
callq 0x6520
movq %rax, %rdi
movq 0x25719(%rip), %rsi     # 0x78f90
callq 0x6570
movq 0x25725(%rip), %rdi     # 0x78fa8
leaq 0x7a1f(%rip), %rsi      # 0x5b2a9
callq 0x6520
movq %rax, %rdi
movq 0x256f7(%rip), %rsi     # 0x78f90
callq 0x6570
movq %rax, %rdi
movq 0x256e8(%rip), %rsi     # 0x78f90
callq 0x6570
xorl %eax, %eax
popq %rbp
retq
nopw %cs:(%rax,%rax)