// File: /workspace/github_c_makefile_star2_O2/nh13[P]ksw/src/main.c
// Function: usage
void usage(main_opt_t *opt)
{
	int i;
	fprintf(stderr, "\n");
	fprintf(stderr, "Program: ksw (klib smith-waterman)\n");
	fprintf(stderr, "Version: %s\n", GIT_HASH);
	fprintf(stderr, "Usage: ksw [options]\n\n");
	fprintf(stderr, "Algorithm options:\n\n");
	fprintf(stderr, "       -M INT      The alignment mode:");
	for (i = AlignmentModeStart; i <= AlignmentModeEnd; ++i) {
		fprintf(stderr, " %d - %s", i, alignment_mode_to_str(i));
		if (i < AlignmentModeEnd) fputc(',', stderr);
	}
	fprintf(stderr, " [%d - %s]\n", opt->alignment_mode, alignment_mode_to_str(opt->alignment_mode));
	fprintf(stderr, "       -a INT      The match score (>0) [%d]\n", opt->match_score);
	fprintf(stderr, "       -b INT      The mismatch penalty (>0) [%d]\n", opt->mismatch_score);
	fprintf(stderr, "       -q INT      The gap open penalty (>=0) [%d]\n", opt->gap_open);
	fprintf(stderr, "       -r INT      The gap extend penalty (>0) [%d]\n", opt->gap_extend);
	fprintf(stderr, "       -w INT      The band width (ksw only) [%d]\n", opt->band_width);
	fprintf(stderr, "       -m FILE     Path to the scoring matrix (4x4 or 5x5) [%s]\n", opt->matrix_fn == NULL ? "None" : opt->matrix_fn);
	fprintf(stderr, "       -c          Append the cigar to the output [%s]\n", opt->add_cigar == 0 ? "false" : "true");
	fprintf(stderr, "       -s          Append the query and target to the output [%s]\n", opt->add_seq == 0 ? "false" : "true");
	fprintf(stderr, "       -H          Add a header line to the output [%s]\n", opt->add_header == 0 ? "false" : "true");
	fprintf(stderr, "       -R          Right-align gaps (ksw only)[%s]\n", opt->right_align_gaps == 0 ? "false" : "true");
	fprintf(stderr, "       -O          Output offset-and-length, otherwise start-and-end (all zero-based)[%s]\n", opt->offset_and_length == 0 ? "false" : "true");
	fprintf(stderr, "       -l INT      The library type:");
	for (i = LibraryStart; i <= LibraryEnd; ++i) {
		fprintf(stderr, " %d - %s", i, library_to_str(i));
		if (i < LibraryEnd) fputc(',', stderr);
	}
	fprintf(stderr, " [%d - %s]\n", opt->library, library_to_str(opt->library));
	fprintf(stderr,"\nNote: when any of the algorithms open a gap, the gap open plus the gap extension penalty is applied.\n");
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %rdi, %rbx
movq 0x593f5a(%rip), %r13    # 0x73afd8
movq (%r13), %rsi
pushq $0xa
popq %rdi
callq 0x19e140
movq (%r13), %rcx
leaq 0x3c1802(%rip), %rdi    # 0x568897
pushq $0x23
popq %rsi
pushq $0x1
popq %r14
movq %r14, %rdx
callq 0x19e200
movq (%r13), %rdi
leaq 0x3c180c(%rip), %rsi    # 0x5688bb
leaq 0x3c1812(%rip), %rdx    # 0x5688c8
xorl %eax, %eax
callq 0x19e180
movq (%r13), %rcx
leaq 0x3c1806(%rip), %rdi    # 0x5688ce
pushq $0x16
popq %rsi
movq %r14, %rdx
callq 0x19e200
movq (%r13), %rcx
leaq 0x3c1807(%rip), %rdi    # 0x5688e5
pushq $0x14
popq %rsi
movq %r14, %rdx
callq 0x19e200
movq (%r13), %rcx
leaq 0x3c1806(%rip), %rdi    # 0x5688fa
pushq $0x26
popq %rsi
movq %r14, %rdx
callq 0x19e200
leaq 0x3c181b(%rip), %r14    # 0x568921
pushq $0x2c
popq %rbp
xorl %r15d, %r15d
movq (%r13), %r12
cmpl $0x4, %r15d
je 0x1a7147
movl %r15d, %edi
callq 0x1a6345
movq %r12, %rdi
movq %r14, %rsi
movl %r15d, %edx
movq %rax, %rcx
xorl %eax, %eax
callq 0x19e180
cmpl $0x3, %r15d
je 0x1a7142
movq (%r13), %rsi
movl %ebp, %edi
callq 0x19e140
incl %r15d
jmp 0x1a710c
movl 0x20(%rbx), %r14d
movl %r14d, %edi
callq 0x1a6345
leaq 0x3c17d0(%rip), %rsi    # 0x56892a
xorl %ebp, %ebp
movq %r12, %rdi
movl %r14d, %edx
movq %rax, %rcx
xorl %eax, %eax
callq 0x19e180
movq (%r13), %rdi
movl (%rbx), %edx
leaq 0x3c17bd(%rip), %rsi    # 0x568936
xorl %eax, %eax
callq 0x19e180
movq (%r13), %rdi
movl 0x4(%rbx), %edx
leaq 0x3c17d6(%rip), %rsi    # 0x568964
xorl %eax, %eax
callq 0x19e180
movq (%r13), %rdi
movl 0x8(%rbx), %edx
leaq 0x3c17f4(%rip), %rsi    # 0x568997
xorl %eax, %eax
callq 0x19e180
movq (%r13), %rdi
movl 0xc(%rbx), %edx
leaq 0x3c1813(%rip), %rsi    # 0x5689cb
xorl %eax, %eax
callq 0x19e180
movq (%r13), %rdi
movl 0x10(%rbx), %edx
leaq 0x3c1833(%rip), %rsi    # 0x568a00
xorl %eax, %eax
callq 0x19e180
movq (%r13), %rdi
movq 0x18(%rbx), %rax
testq %rax, %rax
leaq 0x3c188e(%rip), %rdx    # 0x568a74
cmovneq %rax, %rdx
leaq 0x3c1842(%rip), %rsi    # 0x568a33
xorl %eax, %eax
callq 0x19e180
movq (%r13), %rdi
cmpl $0x0, 0x24(%rbx)
leaq 0x3c18aa(%rip), %r15    # 0x568ab1
leaq 0x3c18a9(%rip), %r14    # 0x568ab7
movq %r14, %rdx
cmoveq %r15, %rdx
leaq 0x3c185d(%rip), %rsi    # 0x568a79
xorl %eax, %eax
callq 0x19e180
cmpl $0x0, 0x28(%rbx)
movq (%r13), %rdi
movq %r14, %rdx
cmoveq %r15, %rdx
leaq 0x3c1883(%rip), %rsi    # 0x568abc
xorl %eax, %eax
callq 0x19e180
cmpl $0x0, 0x2c(%rbx)
movq (%r13), %rdi
movq %r14, %rdx
cmoveq %r15, %rdx
leaq 0x3c18a9(%rip), %rsi    # 0x568aff
xorl %eax, %eax
callq 0x19e180
cmpl $0x0, 0x30(%rbx)
movq (%r13), %rdi
movq %r14, %rdx
cmoveq %r15, %rdx
leaq 0x3c18c5(%rip), %rsi    # 0x568b38
xorl %eax, %eax
callq 0x19e180
movq (%r13), %rdi
cmpl $0x0, 0x34(%rbx)
cmoveq %r15, %r14
leaq 0x3c18df(%rip), %rsi    # 0x568b6c
movq %r14, %rdx
xorl %eax, %eax
callq 0x19e180
movq (%r13), %rcx
leaq 0x3c1925(%rip), %rdi    # 0x568bc7
pushq $0x24
popq %rsi
pushq $0x1
popq %rdx
callq 0x19e200
movq (%r13), %rdi
leaq 0x3c1266(%rip), %r14    # 0x56851e
movl %ebp, %eax
leaq 0x3c115f(%rip), %r15    # 0x568420
movslq (%r15,%rax,4), %rax
addq %r15, %rax
movq %r14, %rcx
jmpq *%rax
leaq 0x3c15a6(%rip), %rcx    # 0x56887a
jmp 0x1a72dd
leaq 0x3c1246(%rip), %rcx    # 0x568523
leaq 0x3c163d(%rip), %rsi    # 0x568921
movl %ebp, %edx
xorl %eax, %eax
callq 0x19e180
cmpl $0x2, %ebp
je 0x1a72fe
movq (%r13), %rsi
pushq $0x2c
popq %rdi
callq 0x19e140
incl %ebp
movq (%r13), %rdi
movl %ebp, %eax
movslq (%r15,%rax,4), %rax
addq %r15, %rax
movq %r14, %rcx
jmpq *%rax
movl 0x38(%rbx), %edx
cmpq $0x2, %rdx
ja 0x1a7328
leaq 0x4e93ce(%rip), %rax    # 0x6906f0
movq (%rax,%rdx,8), %rcx
jmp 0x1a732f
leaq 0x3c11e7(%rip), %rcx    # 0x568516
leaq 0x3c15f4(%rip), %rsi    # 0x56892a
xorl %eax, %eax
callq 0x19e180
movq (%r13), %rcx
leaq 0x3c18a4(%rip), %rdi    # 0x568bec
pushq $0x66
popq %rsi
pushq $0x1
popq %rdx
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
jmp 0x19e200