// File: simonrharris[P]SKA/src/ska.cpp
// Function: fastqHelp()
int fastqHelp(void){
	std::cout << std::endl << "Usage:" << std::endl;
	std::cout << "ska fastq [options] <fastq files>" << std::endl << std::endl;
	std::cout << "Options:" << std::endl;
	std::cout << "-h\t\tPrint this help." << std::endl;
	std::cout << "-a\t\tPrint allele frequencies of split kmers to file [Default = false]" << std::endl;
	std::cout << "-c <int>\tCoverage cutoff. Kmers with coverage below this value will \n\t\tbe discarded. [Default = 4]" << std::endl;
	std::cout << "-C <int>\tFile coverage cutoff. Kmers with coverage below this value \n\t\tin any of the fastq files will be discarded. [Default = 2]" << 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\t[Default = 15]" << std::endl;
	std::cout << "-m <float>\tMinimum allowable minor allele frequency. Kmer alleles below \n\t\tthis frequency will be discarded. [Default = 0.2]" << std::endl;
	std::cout << "-o <file>\tOutput prefix. [Default = fastq]" << std::endl;
	std::cout << "-q <int>\tQuality filter for fastq files. No kmers will be created \n\t\tfrom sequence including quality scores below this cutoff. \n\t\t[Default = 20]" << std::endl << std::endl;
	return 0;
}

// Assembly:
pushq %rbp
movq %rsp, %rbp
movq 0x27e9d(%rip), %rdi     # 0x78fa8
movq 0x27e7e(%rip), %rsi     # 0x78f90
callq 0x6570
movq %rax, %rdi
leaq 0x98df(%rip), %rsi      # 0x5aa00
callq 0x6520
movq %rax, %rdi
movq 0x27e60(%rip), %rsi     # 0x78f90
callq 0x6570
movq 0x27e6c(%rip), %rdi     # 0x78fa8
leaq 0xac1e(%rip), %rsi      # 0x5bd61
callq 0x6520
movq %rax, %rdi
movq 0x27e3e(%rip), %rsi     # 0x78f90
callq 0x6570
movq %rax, %rdi
movq 0x27e2f(%rip), %rsi     # 0x78f90
callq 0x6570
movq 0x27e3b(%rip), %rdi     # 0x78fa8
leaq 0x9ce5(%rip), %rsi      # 0x5ae59
callq 0x6520
movq %rax, %rdi
movq 0x27e0d(%rip), %rsi     # 0x78f90
callq 0x6570
movq 0x27e19(%rip), %rdi     # 0x78fa8
leaq 0x9ccc(%rip), %rsi      # 0x5ae62
callq 0x6520
movq %rax, %rdi
movq 0x27deb(%rip), %rsi     # 0x78f90
callq 0x6570
movq 0x27df7(%rip), %rdi     # 0x78fa8
leaq 0xabcb(%rip), %rsi      # 0x5bd83
callq 0x6520
movq %rax, %rdi
movq 0x27dc9(%rip), %rsi     # 0x78f90
callq 0x6570
movq 0x27dd5(%rip), %rdi     # 0x78fa8
leaq 0xabef(%rip), %rsi      # 0x5bdc9
callq 0x6520
movq %rax, %rdi
movq 0x27da7(%rip), %rsi     # 0x78f90
callq 0x6570
movq 0x27db3(%rip), %rdi     # 0x78fa8
leaq 0xac30(%rip), %rsi      # 0x5be2c
callq 0x6520
movq %rax, %rdi
movq 0x27d85(%rip), %rsi     # 0x78f90
callq 0x6570
movq 0x27d91(%rip), %rdi     # 0x78fa8
leaq 0xa9bc(%rip), %rsi      # 0x5bbda
callq 0x6520
movq %rax, %rdi
movq 0x27d63(%rip), %rsi     # 0x78f90
callq 0x6570
movq 0x27d6f(%rip), %rdi     # 0x78fa8
leaq 0xac6e(%rip), %rsi      # 0x5beae
callq 0x6520
movq %rax, %rdi
movq 0x27d41(%rip), %rsi     # 0x78f90
callq 0x6570
movq 0x27d4d(%rip), %rdi     # 0x78fa8
leaq 0xacc9(%rip), %rsi      # 0x5bf2b
callq 0x6520
movq %rax, %rdi
movq 0x27d1f(%rip), %rsi     # 0x78f90
callq 0x6570
movq 0x27d2b(%rip), %rdi     # 0x78fa8
leaq 0xacd2(%rip), %rsi      # 0x5bf56
callq 0x6520
movq %rax, %rdi
movq 0x27cfd(%rip), %rsi     # 0x78f90
callq 0x6570
movq %rax, %rdi
movq 0x27cee(%rip), %rsi     # 0x78f90
callq 0x6570
xorl %eax, %eax
popq %rbp
retq
nopl (%rax,%rax)