// File: /workspace/github_c_makefile_star2_O3/lh3[P]minimap2/index.c
// Function: mm_idx_jjump_read
int mm_idx_jjump_read(mm_idx_t *mi, const char *fn, int flag, int min_sc)
{
	int32_t i, j, n_anno = 0, n_misc = 0;
	mm_idx_intv_t *I;
	mm_idx_jjump_t *J;
	if (mi->h == 0) mm_idx_index_name(mi);
	I = mm_idx_bed_read_merge(mi, fn, 1, min_sc);
	J = mm_idx_bed2jjump(mi, I, flag);
	for (i = 0; i < mi->n_seq; ++i) free(I[i].a);
	free(I);
	if (mi->J) {
		mm_idx_jjump_t *J2;
		J2 = mm_idx_jjump_merge(mi, mi->J, J);
		for (i = 0; i < mi->n_seq; ++i) {
			free(mi->J[i].a); free(J[i].a);
		}
		free(mi->J); free(J);
		mi->J = J2;
	} else mi->J = J;
	for (i = 0; i < mi->n_seq; ++i) {
		for (j = 0; j < mi->J[i].n; ++j)
			if (mi->J[i].a[j].flag & MM_JUNC_ANNO) ++n_anno;
			else ++n_misc;
	}
	if (mm_verbose >= 3)
		fprintf(stderr, "[%s] there are %d annotated and %d other splice positions in the index\n", __func__, n_anno, n_misc);
	return 0;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x28, %rsp
movl %ecx, %r14d
movl %edx, %ebp
movq %rsi, %r15
movq %rdi, %rbx
cmpq $0x0, 0x58(%rdi)
jne 0x9c27
movq %rbx, %rdi
callq 0x6dec
movq %rbx, %rdi
movq %r15, %rsi
movl $0x1, %edx
movl %r14d, %ecx
callq 0x8f97
movq %rax, (%rsp)
movl 0x10(%rbx), %r12d
movl $0x10, %esi
movq %r12, %rdi
callq 0x2230
movq %rax, 0x8(%rsp)
testq %r12, %r12
movq %rbx, %r14
je 0x9d41
xorl %r13d, %r13d
movq 0x8(%rsp), %r15
movq %r13, %r12
shlq $0x4, %r12
movq (%rsp), %rax
movslq (%rax,%r12), %rbx
leaq (%rbx,%rbx), %rdi
movl %edi, (%r15,%r12)
movl $0x10, %esi
callq 0x2230
movq %rax, 0x8(%r15,%r12)
testq %rbx, %rbx
jle 0x9cf7
movq (%rsp), %rcx
addq %r12, %rcx
movq 0x8(%rcx), %rcx
shlq $0x4, %rbx
xorl %edx, %edx
movl (%rcx,%rdx), %esi
movl %esi, (%rax,%rdx,2)
movl 0x4(%rcx,%rdx), %edi
movl %edi, 0x4(%rax,%rdx,2)
movl 0x8(%rcx,%rdx), %r8d
movl %r8d, 0x8(%rax,%rdx,2)
movl 0xc(%rcx,%rdx), %r9d
sarl $0x1e, %r9d
movw %r9w, 0xc(%rax,%rdx,2)
movw %bp, 0xe(%rax,%rdx,2)
movl %edi, 0x10(%rax,%rdx,2)
movl %esi, 0x14(%rax,%rdx,2)
movl %r8d, 0x18(%rax,%rdx,2)
movl 0xc(%rcx,%rdx), %esi
sarl $0x1e, %esi
movw %si, 0x1c(%rax,%rdx,2)
movw %bp, 0x1e(%rax,%rdx,2)
addq $0x10, %rdx
cmpq %rdx, %rbx
jne 0x9ca4
movq 0x8(%rsp), %r15
addq %r15, %r12
movq %r12, %rdi
callq 0xab6a
incq %r13
movl 0x10(%r14), %eax
cmpq %rax, %r13
jb 0x9c68
testl %eax, %eax
je 0x9d41
movq (%rsp), %r12
addq $0x8, %r12
xorl %r13d, %r13d
movq (%r12), %rdi
callq 0x2040
incq %r13
movl 0x10(%r14), %ebx
addq $0x10, %r12
cmpq %rbx, %r13
jb 0x9d26
jmp 0x9d43
xorl %ebx, %ebx
movq (%rsp), %rdi
callq 0x2040
movq 0x48(%r14), %r12
testq %r12, %r12
je 0x9e9d
movl %ebx, %edi
movl $0x10, %esi
callq 0x2230
movq %rax, %r13
testl %ebx, %ebx
movq 0x8(%rsp), %r15
je 0x9e86
movq %r12, 0x20(%rsp)
movq %r13, 0x18(%rsp)
xorl %ebx, %ebx
movq %r14, 0x10(%rsp)
movq 0x18(%rsp), %rbp
movq %rbx, (%rsp)
shlq $0x4, %rbx
leaq (%r15,%rbx), %r13
leaq (%rbx,%rbp), %r12
movq 0x20(%rsp), %rax
movl (%rax,%rbx), %r14d
movl (%r15,%rbx), %r15d
leal (%r15,%r14), %eax
movl %eax, (%rbp,%rbx)
movslq %eax, %rdi
movl $0x10, %esi
callq 0x2230
movq %rax, 0x8(%rbp,%rbx)
testl %r14d, %r14d
jle 0x9df6
addq 0x20(%rsp), %rbx
xorl %ecx, %ecx
xorl %eax, %eax
movq 0x8(%r12), %rdx
incq %rax
movq 0x8(%rbx), %rsi
movups (%rsi,%rcx), %xmm0
movups %xmm0, (%rdx,%rcx)
movslq (%rbx), %rdx
addq $0x10, %rcx
cmpq %rdx, %rax
jl 0x9dd0
movl (%r13), %r15d
jmp 0x9df8
xorl %eax, %eax
movq 0x10(%rsp), %r14
testl %r15d, %r15d
movq (%rsp), %rbx
jle 0x9e32
shlq $0x4, %rax
xorl %ecx, %ecx
xorl %edx, %edx
movq 0x8(%r12), %rsi
addq %rax, %rsi
movq 0x8(%r13), %rdi
movups (%rdi,%rcx), %xmm0
movups %xmm0, (%rcx,%rsi)
incq %rdx
movslq (%r13), %rsi
addq $0x10, %rcx
cmpq %rsi, %rdx
jl 0x9e0e
movq %r12, %rdi
callq 0xab6a
incq %rbx
movl 0x10(%r14), %eax
cmpq %rax, %rbx
movq 0x8(%rsp), %r15
jb 0x9d8b
testl %eax, %eax
movq 0x18(%rsp), %r13
je 0x9e86
movl $0x8, %ebx
xorl %r12d, %r12d
movq 0x48(%r14), %rax
movq (%rax,%rbx), %rdi
callq 0x2040
movq (%r15,%rbx), %rdi
callq 0x2040
incq %r12
movl 0x10(%r14), %eax
addq $0x10, %rbx
cmpq %rax, %r12
jb 0x9e60
movq 0x48(%r14), %rdi
callq 0x2040
movq %r15, %rdi
callq 0x2040
movl 0x10(%r14), %ebx
jmp 0x9ea2
movq 0x8(%rsp), %r13
movq %r13, 0x48(%r14)
testl %ebx, %ebx
je 0x9ef9
movl %ebx, %eax
xorl %edx, %edx
xorl %ecx, %ecx
xorl %r8d, %r8d
movq %rdx, %rdi
shlq $0x4, %rdi
movslq (%r13,%rdi), %rsi
testq %rsi, %rsi
jle 0x9eef
addq %r13, %rdi
movq 0x8(%rdi), %rdi
shlq $0x4, %rsi
xorl %r9d, %r9d
movzwl 0xe(%rdi,%r9), %r10d
andl $0x1, %r10d
addl %r10d, %ecx
xorl $0x1, %r10d
addl %r10d, %r8d
addq $0x10, %r9
cmpq %r9, %rsi
jne 0x9ed2
incq %rdx
cmpq %rax, %rdx
jne 0x9eb3
jmp 0x9efe
xorl %r8d, %r8d
xorl %ecx, %ecx
leaq 0x2c7fb(%rip), %rax     # 0x36700
cmpl $0x3, (%rax)
jge 0x9f1b
xorl %eax, %eax
addq $0x28, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0x2c0d6(%rip), %rax     # 0x35ff8
movq (%rax), %rdi
leaq 0x235a2(%rip), %rsi     # 0x2d4ce
leaq 0x235e3(%rip), %rdx     # 0x2d516
xorl %eax, %eax
callq 0x2260
jmp 0x9f0a