// File: /workspace/github_cpp_makefile_star2_O3/afinit[P]afin/process.cpp
// Function: Process::start_run()
void Process::start_run(){
  // initialize logfile if logging enabled
  if( log_output || screen_output ){
    logfile_init();
  }

  // prevent printing of 
  if( no_fusion )
    print_fused = 0;

  // log output file
  Log::Inst()->log_it( string("output file: ") + outfile );
  
  // initialize objects
  reads = new Readlist( readsfiles ); 
  contigs = new Contiglist( reads, contigsfiles, outfile );
  fuse = new Fusion( contigs, reads );

  Log::Inst()->log_it( "End initialization phase" );
  
  // make initial attempt to fuse contigs  
  if( ! no_fusion )
    fuse->run_fusion( true );
  
  if( test_run )
    contigs->output_contigs( 0, outfile + ".fus", "mid" );

  run_manager();

  contigs->create_final_fasta();
}

// Assembly:
pushq %rbp
movq %rsp, %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x108, %rsp            # imm = 0x108
movq %rdi, %rbx
movl 0x15a8b(%rip), %eax     # 0x1d640
orl 0x15a89(%rip), %eax     # 0x1d644
je 0x7bc5
movq %rbx, %rdi
callq 0x6e3a
cmpl $0x0, 0x15a80(%rip)     # 0x1d64c
je 0x7bd8
movl $0x0, 0x15a64(%rip)     # 0x1d63c
callq 0x9692
movq %rax, %r14
leaq -0xf8(%rbp), %r15
movq %r15, -0x10(%r15)
leaq 0xe0e7(%rip), %rsi      # 0x15cd9
leaq 0xe0ed(%rip), %rdx      # 0x15ce6
leaq -0x108(%rbp), %rdi
callq 0x6be0
movq 0x18(%rbx), %rsi
movq 0x20(%rbx), %rdx
leaq -0x108(%rbp), %rdi
callq 0x40f0
leaq -0x58(%rbp), %r12
movq %r12, -0x10(%r12)
movq (%rax), %rdx
movq %rax, %rcx
addq $0x10, %rcx
cmpq %rcx, %rdx
je 0x7c3e
movq %rdx, -0x68(%rbp)
movq (%rcx), %rdx
movq %rdx, -0x58(%rbp)
jmp 0x7c46
movups (%rcx), %xmm0
movups %xmm0, (%r12)
movq 0x8(%rax), %rdx
leaq -0x68(%rbp), %rsi
movq %rdx, 0x8(%rsi)
movq %rcx, (%rax)
movq $0x0, 0x8(%rax)
movb $0x0, 0x10(%rax)
movq %r14, %rdi
callq 0x98ba
movq -0x68(%rbp), %rdi
cmpq %r12, %rdi
je 0x7c77
callq 0x42f0
movq -0x108(%rbp), %rdi
cmpq %r15, %rdi
je 0x7c88
callq 0x42f0
movl $0x38, %edi
callq 0x4310
movq %rax, %r14
leaq -0xd8(%rbp), %r15
movq %r15, -0x10(%r15)
movq 0x38(%rbx), %rsi
movq 0x40(%rbx), %rdx
addq %rsi, %rdx
leaq -0xe8(%rbp), %rdi
callq 0x68f6
leaq -0xe8(%rbp), %rsi
movq %r14, %rdi
callq 0xe8d0
movq %r14, (%rbx)
movq -0xe8(%rbp), %rdi
cmpq %r15, %rdi
je 0x7cdd
callq 0x42f0
movq (%rbx), %r14
movl $0x58, %edi
callq 0x4310
movq %rax, %r15
leaq -0xb8(%rbp), %r12
movq %r12, -0x10(%r12)
movq 0x58(%rbx), %rsi
movq 0x60(%rbx), %rdx
addq %rsi, %rdx
leaq -0xc8(%rbp), %rdi
callq 0x68f6
leaq -0x98(%rbp), %r13
movq %r13, -0x10(%r13)
movq 0x18(%rbx), %rsi
movq 0x20(%rbx), %rdx
addq %rsi, %rdx
leaq -0xa8(%rbp), %rdi
callq 0x68f6
leaq -0xc8(%rbp), %rdx
leaq -0xa8(%rbp), %rcx
movq %r15, %rdi
movq %r14, %rsi
callq 0x13470
movq %r15, 0x8(%rbx)
movq -0xa8(%rbp), %rdi
cmpq %r13, %rdi
je 0x7d5d
callq 0x42f0
movq -0xc8(%rbp), %rdi
cmpq %r12, %rdi
je 0x7d6e
callq 0x42f0
movl $0x40, %edi
callq 0x4310
movq %rax, %r14
movq (%rbx), %rdx
movq 0x8(%rbx), %rsi
movq %rax, %rdi
callq 0xa200
movq %r14, 0x10(%rbx)
callq 0x9692
movq %rax, %r14
leaq -0x118(%rbp), %r12
movq %r12, -0x10(%r12)
leaq 0xdf3e(%rip), %rsi      # 0x15ce7
leaq 0xdf4f(%rip), %rdx      # 0x15cff
leaq -0x128(%rbp), %r15
movq %r15, %rdi
callq 0x6be0
movq %r14, %rdi
movq %r15, %rsi
callq 0x98ba
movq -0x128(%rbp), %rdi
cmpq %r12, %rdi
je 0x7ddb
callq 0x42f0
cmpl $0x0, 0x1586a(%rip)     # 0x1d64c
jne 0x7df2
movq 0x10(%rbx), %rdi
movl $0x1, %esi
callq 0xd184
cmpb $0x1, 0x1583f(%rip)     # 0x1d638
jne 0x7e88
movq 0x8(%rbx), %r14
leaq -0x38(%rbp), %r12
movq %r12, -0x10(%r12)
movq 0x18(%rbx), %rsi
movq 0x20(%rbx), %rdx
addq %rsi, %rdx
leaq -0x48(%rbp), %r15
movq %r15, %rdi
callq 0x68f6
leaq 0xded6(%rip), %rsi      # 0x15d00
movq %r15, %rdi
callq 0x45f0
leaq -0x78(%rbp), %r15
movq %r15, -0x10(%r15)
leaq 0xdec4(%rip), %rsi      # 0x15d05
leaq 0xdec0(%rip), %rdx      # 0x15d08
leaq -0x88(%rbp), %rdi
callq 0x6be0
leaq -0x48(%rbp), %rdx
leaq -0x88(%rbp), %rcx
movq %r14, %rdi
xorl %esi, %esi
callq 0x13f20
movq -0x88(%rbp), %rdi
cmpq %r15, %rdi
je 0x7e7a
callq 0x42f0
movq -0x48(%rbp), %rdi
cmpq %r12, %rdi
je 0x7e88
callq 0x42f0
movq %rbx, %rdi
callq 0x7f66
movq 0x8(%rbx), %rdi
callq 0x141f8
addq $0x108, %rsp            # imm = 0x108
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq %rax, %rbx
movq -0x88(%rbp), %rdi
cmpq %r15, %rdi
je 0x7ec6
callq 0x42f0
jmp 0x7ec6
jmp 0x7ec3
movq %rax, %rbx
movq -0x48(%rbp), %rdi
jmp 0x7ed6
movq %rax, %rbx
movq -0x128(%rbp), %rdi
cmpq %r12, %rdi
jne 0x7f53
jmp 0x7f58
jmp 0x7f29
movq %rax, %rbx
movq -0xa8(%rbp), %rdi
cmpq %r13, %rdi
je 0x7ef8
callq 0x42f0
jmp 0x7ef8
movq %rax, %rbx
movq -0xc8(%rbp), %rdi
cmpq %r12, %rdi
je 0x7f0e
callq 0x42f0
jmp 0x7f0e
movq %rax, %rbx
movq %r15, %rdi
jmp 0x7f53
movq %rax, %rbx
movq -0xe8(%rbp), %rdi
cmpq %r15, %rdi
je 0x7f2c
callq 0x42f0
jmp 0x7f2c
movq %rax, %rbx
movq %r14, %rdi
jmp 0x7f53
movq %rax, %rbx
movq -0x68(%rbp), %rdi
cmpq %r12, %rdi
je 0x7f47
callq 0x42f0
jmp 0x7f47
movq %rax, %rbx
movq -0x108(%rbp), %rdi
cmpq %r15, %rdi
je 0x7f58
callq 0x42f0
movq %rbx, %rdi
callq 0x4590
movq %rax, %rbx
jmp 0x7f58
nop