// File: /workspace/github_cpp_makefile_star2_O1/zeeev[P]DASVC/bamtools/src/toolkit/bamtools_index.cpp
// Function: BamTools::IndexTool::IndexTool()
IndexTool::IndexTool(void)
    : AbstractTool()
    , m_settings(new IndexSettings)
    , m_impl(0)
{
    // set program details
    Options::SetProgramInfo("bamtools index", "creates index for BAM file", "[-in <filename>] [-bti]");
    
    // set up options 
    OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
    Options::AddValueOption("-in", "BAM filename", "the input BAM file", "", m_settings->HasInputBamFilename, m_settings->InputBamFilename, IO_Opts, Options::StandardIn());
    Options::AddOption("-bti", "create (non-standard) BamTools index file (*.bti). Default behavior is to create standard BAM index (*.bai)", m_settings->IsUsingBamtoolsIndex, IO_Opts);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x88, %rsp
movq %rdi, %rbx
leaq 0x4c325(%rip), %rax     # 0x8f9b0
movq %rax, (%rdi)
movl $0x28, %edi
callq 0x275c0
movq %rax, %r14
movw $0x0, (%rax)
callq 0x646e2
leaq 0x8(%r14), %rdi
movq %r14, %rcx
addq $0x18, %rcx
movq %rcx, 0x8(%r14)
movq (%rax), %rsi
movq 0x8(%rax), %rdx
addq %rsi, %rdx
callq 0x2f122
movq %r14, 0x8(%rbx)
movq $0x0, 0x10(%rbx)
leaq 0x18(%rsp), %r12
movq %r12, -0x10(%r12)
leaq 0x3025d(%rip), %rsi     # 0x7393d
leaq 0x30264(%rip), %rdx     # 0x7394b
leaq 0x8(%rsp), %rdi
callq 0x2f1b2
leaq 0x38(%rsp), %r15
movq %r15, -0x10(%r15)
leaq 0x3024b(%rip), %rsi     # 0x7394c
leaq 0x3025e(%rip), %rdx     # 0x73966
leaq 0x28(%rsp), %rdi
callq 0x2f1b2
leaq 0x58(%rsp), %rbp
movq %rbp, -0x10(%rbp)
leaq 0x30245(%rip), %rsi     # 0x73967
leaq 0x30255(%rip), %rdx     # 0x7397e
leaq 0x48(%rsp), %rdi
callq 0x2f1b2
leaq 0x8(%rsp), %rdi
leaq 0x28(%rsp), %rsi
leaq 0x48(%rsp), %rdx
callq 0x646a4
movq 0x48(%rsp), %rdi
cmpq %rbp, %rdi
je 0x43756
callq 0x27560
movq 0x28(%rsp), %rdi
cmpq %r15, %rdi
je 0x43765
callq 0x27560
movq 0x8(%rsp), %rdi
cmpq %r12, %rdi
je 0x43774
callq 0x27560
leaq 0x8(%rsp), %rdi
movq %r12, (%rdi)
leaq 0x2ed8e(%rip), %rsi     # 0x72511
leaq 0x2ed95(%rip), %rdx     # 0x7251f
callq 0x2f1b2
leaq 0x8(%rsp), %rdi
callq 0x63a0c
movq %rax, %r14
movq 0x8(%rsp), %rdi
cmpq %r12, %rdi
je 0x437ab
callq 0x27560
leaq 0x8(%rsp), %rdi
movq %r12, (%rdi)
leaq 0x2ed66(%rip), %rsi     # 0x72520
leaq 0x2ed62(%rip), %rdx     # 0x72523
callq 0x2f1b2
leaq 0x28(%rsp), %rdi
movq %r15, (%rdi)
leaq 0x2ed4f(%rip), %rsi     # 0x72524
leaq 0x2ed54(%rip), %rdx     # 0x72530
callq 0x2f1b2
leaq 0x48(%rsp), %rdi
movq %rbp, (%rdi)
leaq 0x32fce(%rip), %rsi     # 0x767be
leaq 0x32fd9(%rip), %rdx     # 0x767d0
callq 0x2f1b2
movq %r15, %r12
leaq 0x78(%rsp), %r13
movq %r13, -0x10(%r13)
leaq 0x3400c(%rip), %rdx     # 0x7781b
leaq 0x68(%rsp), %rdi
movq %rdx, %rsi
callq 0x2f1b2
movq 0x8(%rbx), %r15
callq 0x646e2
leaq 0x8(%r15), %r9
leaq 0x8(%rsp), %rdi
leaq 0x28(%rsp), %rsi
leaq 0x48(%rsp), %rdx
leaq 0x68(%rsp), %rcx
movq %r15, %r8
pushq %rax
pushq %r14
callq 0x2ebcc
addq $0x10, %rsp
movq 0x68(%rsp), %rdi
cmpq %r13, %rdi
je 0x4385b
callq 0x27560
movq 0x48(%rsp), %rdi
cmpq %rbp, %rdi
leaq 0x18(%rsp), %r15
je 0x4386f
callq 0x27560
movq 0x28(%rsp), %rdi
cmpq %r12, %rdi
je 0x4387e
callq 0x27560
movq 0x8(%rsp), %rdi
cmpq %r15, %rdi
je 0x4388d
callq 0x27560
leaq 0x8(%rsp), %rdi
movq %r15, (%rdi)
leaq 0x300e3(%rip), %rsi     # 0x7397f
leaq 0x300e0(%rip), %rdx     # 0x73983
callq 0x2f1b2
leaq 0x28(%rsp), %rdi
movq %r12, (%rdi)
leaq 0x300cd(%rip), %rsi     # 0x73984
leaq 0x30131(%rip), %rdx     # 0x739ef
callq 0x2f1b2
movq 0x8(%rbx), %rdx
incq %rdx
leaq 0x8(%rsp), %rdi
leaq 0x28(%rsp), %rsi
movq %r14, %rcx
callq 0x63808
movq 0x28(%rsp), %rdi
cmpq %r12, %rdi
je 0x438eb
callq 0x27560
movq 0x8(%rsp), %rdi
cmpq %r15, %rdi
je 0x438fa
callq 0x27560
addq $0x88, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq %rax, %rbx
movq 0x28(%rsp), %rdi
cmpq %r12, %rdi
je 0x43923
callq 0x27560
jmp 0x43923
movq %rax, %rbx
movq 0x8(%rsp), %rdi
leaq 0x18(%rsp), %rax
cmpq %rax, %rdi
je 0x439f4
jmp 0x439ef
jmp 0x439a3
movq %rax, %rbx
jmp 0x439ba
movq %r15, %r12
movq %rax, %rbx
jmp 0x439c9
movq %rax, %rbx
jmp 0x439d8
jmp 0x439a3
movq %rax, %rbx
movq 0x8(%rsp), %rdi
cmpq %r12, %rdi
je 0x439f4
jmp 0x439ef
jmp 0x439a3
movq %rax, %rbx
movq 0x48(%rsp), %rdi
cmpq %rbp, %rdi
je 0x43983
callq 0x27560
jmp 0x43983
movq %rax, %rbx
movq 0x28(%rsp), %rdi
cmpq %r15, %rdi
je 0x43997
callq 0x27560
jmp 0x43997
movq %rax, %rbx
movq 0x8(%rsp), %rdi
cmpq %r12, %rdi
je 0x439f4
jmp 0x439ef
movq %rax, %rbx
jmp 0x439f4
movq %rax, %rbx
movq 0x68(%rsp), %rdi
cmpq %r13, %rdi
je 0x439ba
callq 0x27560
movq 0x48(%rsp), %rdi
cmpq %rbp, %rdi
je 0x439c9
callq 0x27560
movq 0x28(%rsp), %rdi
cmpq %r12, %rdi
je 0x439d8
callq 0x27560
movq 0x8(%rsp), %rdi
leaq 0x18(%rsp), %rax
cmpq %rax, %rdi
je 0x439f4
jmp 0x439ef
movq %rax, %rbx
movq %r14, %rdi
callq 0x27560
movq %rbx, %rdi
callq 0x27b20