// File: /workspace/github_c_makefile_star2_O2/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 0x8ac2
movq %rbx, %rdi
callq 0x5daa
pushq $0x1
popq %rdx
movq %rbx, %rdi
movq %r15, %rsi
movl %r14d, %ecx
callq 0x7e89
movq %rax, (%rsp)
movl 0x10(%rbx), %r12d
pushq $0x10
popq %rsi
movq %r12, %rdi
callq 0x2230
movq %rax, 0x8(%rsp)
xorl %r13d, %r13d
movq %rbx, %r14
movq %rbx, 0x18(%rsp)
movl %r12d, %eax
cmpq %rax, %r13
jae 0x8bc3
movq %r13, %r14
shlq $0x4, %r14
movq (%rsp), %rax
leaq (%rax,%r14), %rbx
movq 0x8(%rsp), %r12
leaq (%r12,%r14), %rcx
movq %rcx, 0x10(%rsp)
movslq (%rax,%r14), %r15
movq %r15, %rdi
addq %r15, %rdi
movl %edi, (%r12,%r14)
pushq $0x10
popq %rsi
callq 0x2230
movq %rax, 0x8(%r12,%r14)
movq 0x18(%rsp), %r14
testl %r15d, %r15d
movl $0x0, %ecx
cmovgl %r15d, %ecx
shlq $0x4, %rcx
xorl %edx, %edx
cmpq %rdx, %rcx
je 0x8bad
movq 0x8(%rbx), %rsi
movl (%rsi,%rdx), %edi
movl %edi, (%rax,%rdx,2)
movl 0x4(%rsi,%rdx), %r8d
movl %r8d, 0x4(%rax,%rdx,2)
movl 0x8(%rsi,%rdx), %r9d
movl %r9d, 0x8(%rax,%rdx,2)
movl 0xc(%rsi,%rdx), %r10d
sarl $0x1e, %r10d
movw %r10w, 0xc(%rax,%rdx,2)
movw %bp, 0xe(%rax,%rdx,2)
movl %r8d, 0x10(%rax,%rdx,2)
movl %edi, 0x14(%rax,%rdx,2)
movl %r9d, 0x18(%rax,%rdx,2)
movl 0xc(%rsi,%rdx), %esi
sarl $0x1e, %esi
movw %si, 0x1c(%rax,%rdx,2)
movw %bp, 0x1e(%rax,%rdx,2)
addq $0x10, %rdx
jmp 0x8b51
movq 0x10(%rsp), %rdi
callq 0x98fe
incq %r13
movl 0x10(%r14), %r12d
jmp 0x8af6
movq (%rsp), %rbx
addq $0x8, %rbx
xorl %r13d, %r13d
movl %r12d, %ebp
cmpq %rbp, %r13
jae 0x8beb
movq (%rbx), %rdi
callq 0x2040
incq %r13
movl 0x10(%r14), %r12d
addq $0x10, %rbx
jmp 0x8bce
movq (%rsp), %rdi
callq 0x2040
movq 0x48(%r14), %rax
movq %rax, 0x20(%rsp)
testq %rax, %rax
je 0x8d22
pushq $0x10
popq %rsi
movq %rbp, %rdi
callq 0x2230
movq %rax, (%rsp)
xorl %ebp, %ebp
movq (%rsp), %r15
movl %r12d, %eax
cmpq %rax, %rbp
jae 0x8cd3
movq %rbp, 0x10(%rsp)
shlq $0x4, %rbp
movq 0x20(%rsp), %rcx
leaq (%rcx,%rbp), %rbx
movq 0x8(%rsp), %rax
leaq (%rax,%rbp), %r13
leaq (%r15,%rbp), %r12
movslq (%rcx,%rbp), %r14
movslq (%rax,%rbp), %rdi
addq %r14, %rdi
movl %edi, (%r15,%rbp)
pushq $0x10
popq %rsi
callq 0x2230
movq %rax, 0x8(%r15,%rbp)
xorl %eax, %eax
xorl %ecx, %ecx
movslq %r14d, %rdx
cmpq %rdx, %rcx
jge 0x8c8b
movq 0x8(%r12), %rdx
incq %rcx
movq 0x8(%rbx), %rsi
movups (%rsi,%rax), %xmm0
movups %xmm0, (%rdx,%rax)
movl (%rbx), %r14d
addq $0x10, %rax
jmp 0x8c66
xorl %ecx, %ecx
xorl %edx, %edx
movq 0x18(%rsp), %r14
movq 0x10(%rsp), %rbp
movslq (%r13), %rsi
cmpq %rsi, %rdx
jge 0x8cbf
movq 0x8(%r12), %rsi
addq %rax, %rsi
movq 0x8(%r13), %rdi
movups (%rdi,%rcx), %xmm0
movups %xmm0, (%rcx,%rsi)
incq %rdx
addq $0x10, %rcx
jmp 0x8c99
movq %r12, %rdi
callq 0x98fe
incq %rbp
movl 0x10(%r14), %r12d
jmp 0x8c1b
pushq $0x8
popq %rbx
xorl %r13d, %r13d
movq (%rsp), %r15
movl %r12d, %eax
movq 0x48(%r14), %rdi
cmpq %rax, %r13
jae 0x8d0d
movq (%rdi,%rbx), %rdi
callq 0x2040
movq 0x8(%rsp), %rax
movq (%rax,%rbx), %rdi
callq 0x2040
incq %r13
movl 0x10(%r14), %r12d
addq $0x10, %rbx
jmp 0x8cdd
callq 0x2040
movq 0x8(%rsp), %rdi
callq 0x2040
movl 0x10(%r14), %ebp
jmp 0x8d27
movq 0x8(%rsp), %r15
movq %r15, 0x48(%r14)
xorl %eax, %eax
xorl %edx, %edx
xorl %r8d, %r8d
xorl %ecx, %ecx
cmpq %rbp, %rdx
je 0x8d7c
movq %rdx, %rdi
shlq $0x4, %rdi
leaq (%r15,%rdi), %rsi
movl (%r15,%rdi), %edi
testl %edi, %edi
cmovlel %eax, %edi
shlq $0x4, %rdi
xorl %r9d, %r9d
cmpq %r9, %rdi
je 0x8d77
movq 0x8(%rsi), %r10
movzwl 0xe(%r10,%r9), %r10d
andl $0x1, %r10d
addl %r10d, %ecx
xorl $0x1, %r10d
addl %r10d, %r8d
addq $0x10, %r9
jmp 0x8d54
incq %rdx
jmp 0x8d34
leaq 0x2997d(%rip), %rax     # 0x32700
cmpl $0x3, (%rax)
jge 0x8d99
xorl %eax, %eax
addq $0x28, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0x29258(%rip), %rax     # 0x31ff8
movq (%rax), %rdi
leaq 0x1f724(%rip), %rsi     # 0x284ce
leaq 0x1f765(%rip), %rdx     # 0x28516
xorl %eax, %eax
callq 0x2260
jmp 0x8d88