// File: /workspace/github_c_makefile_star2_O1/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, (%rsp)
movq 0x603ca6(%rip), %r12    # 0x7a1fd8
movq (%r12), %rsi
pushq $0xa
popq %rdi
callq 0x19e140
movq (%r12), %rcx
leaq 0x3f854e(%rip), %rdi    # 0x596897
pushq $0x23
popq %rsi
pushq $0x1
popq %r14
movq %r14, %rdx
callq 0x19e200
movq (%r12), %rdi
leaq 0x3f8558(%rip), %rsi    # 0x5968bb
leaq 0x3f855e(%rip), %rdx    # 0x5968c8
xorl %eax, %eax
callq 0x19e180
movq (%r12), %rcx
leaq 0x3f8552(%rip), %rdi    # 0x5968ce
pushq $0x16
popq %rsi
movq %r14, %rdx
callq 0x19e200
movq (%r12), %rcx
leaq 0x3f8553(%rip), %rdi    # 0x5968e5
pushq $0x14
popq %rsi
movq %r14, %rdx
callq 0x19e200
movq (%r12), %rcx
leaq 0x3f8552(%rip), %rdi    # 0x5968fa
pushq $0x26
popq %rsi
movq %r14, %rdx
callq 0x19e200
leaq 0x559316(%rip), %r13    # 0x6f76d0
leaq 0x3f8155(%rip), %rbx    # 0x596516
leaq 0x3f8559(%rip), %r14    # 0x596921
pushq $0x2c
popq %rbp
xorl %r15d, %r15d
movq %rbx, %rcx
cmpl $0x3, %r15d
ja 0x19e3db
movq (%r13), %rcx
movq (%r12), %rdi
movq %r14, %rsi
movl %r15d, %edx
xorl %eax, %eax
callq 0x19e180
cmpl $0x3, %r15d
je 0x19e3fd
movq (%r12), %rsi
movl %ebp, %edi
callq 0x19e140
incl %r15d
addq $0x8, %r13
cmpl $0x4, %r15d
jne 0x19e3ce
movq (%r12), %rdi
movq (%rsp), %rax
movl 0x20(%rax), %edx
leaq 0x3f80fa(%rip), %r13    # 0x596516
movq %r13, %rcx
cmpq $0x3, %rdx
ja 0x19e430
leaq 0x5592a4(%rip), %rax    # 0x6f76d0
movq (%rax,%rdx,8), %rcx
leaq 0x3f84f3(%rip), %rsi    # 0x59692a
xorl %eax, %eax
callq 0x19e180
movq (%r12), %rdi
movq (%rsp), %rbx
movl (%rbx), %edx
leaq 0x3f84e7(%rip), %rsi    # 0x596936
xorl %eax, %eax
callq 0x19e180
movq (%r12), %rdi
movl 0x4(%rbx), %edx
leaq 0x3f8500(%rip), %rsi    # 0x596964
xorl %eax, %eax
callq 0x19e180
movq (%r12), %rdi
movl 0x8(%rbx), %edx
leaq 0x3f851e(%rip), %rsi    # 0x596997
xorl %eax, %eax
callq 0x19e180
movq (%r12), %rdi
movl 0xc(%rbx), %edx
leaq 0x3f853d(%rip), %rsi    # 0x5969cb
xorl %eax, %eax
callq 0x19e180
movq (%r12), %rdi
movl 0x10(%rbx), %edx
leaq 0x3f855d(%rip), %rsi    # 0x596a00
xorl %eax, %eax
callq 0x19e180
movq (%r12), %rdi
movq 0x18(%rbx), %rax
testq %rax, %rax
leaq 0x3f85b8(%rip), %rdx    # 0x596a74
cmovneq %rax, %rdx
leaq 0x3f856c(%rip), %rsi    # 0x596a33
xorl %eax, %eax
callq 0x19e180
movq (%r12), %rdi
cmpl $0x0, 0x24(%rbx)
leaq 0x3f85d4(%rip), %r15    # 0x596ab1
leaq 0x3f85d3(%rip), %r14    # 0x596ab7
movq %r14, %rdx
cmoveq %r15, %rdx
leaq 0x3f8587(%rip), %rsi    # 0x596a79
xorl %eax, %eax
callq 0x19e180
cmpl $0x0, 0x28(%rbx)
movq (%r12), %rdi
movq %r14, %rdx
cmoveq %r15, %rdx
leaq 0x3f85ad(%rip), %rsi    # 0x596abc
xorl %eax, %eax
callq 0x19e180
cmpl $0x0, 0x2c(%rbx)
movq (%r12), %rdi
movq %r14, %rdx
cmoveq %r15, %rdx
leaq 0x3f85d3(%rip), %rsi    # 0x596aff
xorl %eax, %eax
callq 0x19e180
cmpl $0x0, 0x30(%rbx)
movq (%r12), %rdi
movq %r14, %rdx
cmoveq %r15, %rdx
leaq 0x3f85ef(%rip), %rsi    # 0x596b38
xorl %eax, %eax
callq 0x19e180
movq (%r12), %rdi
cmpl $0x0, 0x34(%rbx)
cmoveq %r15, %r14
leaq 0x3f8609(%rip), %rsi    # 0x596b6c
movq %r14, %rdx
xorl %eax, %eax
callq 0x19e180
movq (%r12), %rcx
leaq 0x3f864f(%rip), %rdi    # 0x596bc7
pushq $0x24
popq %rsi
pushq $0x1
popq %rdx
callq 0x19e200
leaq 0x559166(%rip), %rbx    # 0x6f76f0
leaq 0x3f8390(%rip), %r14    # 0x596921
pushq $0x2c
popq %rbp
xorl %r15d, %r15d
movq %r13, %rcx
cmpl $0x2, %r15d
ja 0x19e5a3
movq (%rbx), %rcx
movq (%r12), %rdi
movq %r14, %rsi
movl %r15d, %edx
xorl %eax, %eax
callq 0x19e180
cmpl $0x2, %r15d
je 0x19e5c5
movq (%r12), %rsi
movl %ebp, %edi
callq 0x19e140
incl %r15d
addq $0x8, %rbx
cmpl $0x3, %r15d
jne 0x19e597
movq (%r12), %rdi
movq (%rsp), %rax
movl 0x38(%rax), %edx
cmpq $0x2, %rdx
ja 0x19e5f0
leaq 0x559106(%rip), %rax    # 0x6f76f0
movq (%rax,%rdx,8), %rcx
jmp 0x19e5f7
leaq 0x3f7f1f(%rip), %rcx    # 0x596516
leaq 0x3f832c(%rip), %rsi    # 0x59692a
xorl %eax, %eax
callq 0x19e180
movq (%r12), %rcx
leaq 0x3f85dc(%rip), %rdi    # 0x596bec
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