// File: /workspace/github_cpp_makefile_star2_O1/afinit[P]afin/afin.cpp
// Function: print_usage(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>)
void print_usage( string prog ){
  cout << "Usage: " << prog << " -c contigsfile(s) -r readsfile(s) [-o outfile] [-m sort_char] [-s sub_len]" << endl;
  cout << "          [-l search_loops] [-i min_cov] [-p min_overlap] [-t max_threads]" << endl;
  cout << "          [-d initial_trim] [-e max_missed] [-f stop_ext] [-g mismatch] [-x extend_len]" << endl;
  cout << "          [--silent] [--no_log] [--no_fusion] [--verbose] [--print_fused]" << endl << endl;
  cout << "       " << prog << " -h [--help]" << endl << endl;
  cout << endl;
  cout << "  -c, contigsfiles       Space (or comma) separated list of files containing contigs" << endl;
  cout << "  -r, readsfiles         Space (or comma) separated list of files containing reads" << endl;
  cout << "  -o, outfile            Output will be printed to the outfile specified, with a .fa extension for the contigs and .log extension for the logfile" << endl;
  cout << "  -m, sort_char          [default:   4] Sorts the reads by the first max_sort_char characters" << endl;
  cout << "  -s, sub_len            [default: 100] Will focus on the current last contig_sub_len characters of the contig in each search" << endl;
  cout << "  -l, search_loops       [default:  10] Will search against each contig a maximum of max_search_loops times to attempt extension" << endl;
  cout << "  -i, min_cov            [default:   3] Will stop adding bp's once the coverage falls below min_cov" << endl;
  cout << "  -p, min_overlap        [default:  20] Only those reads overlapping the contig by at least min_overlap bp's will be returned in each search" << endl;
  cout << "  -t, max_threads        [default:   4] Will only run max_threads threads at a time" << endl;
  cout << "  -d, initial_trim       [default:   0] Length to trim off the beginning and end of each contig at the start of the program" << endl;
  cout << "  -e, max_missed         [default:   5] Maximum allowable mismatched bp's for each read when checking troubled contig fusions" << endl;
  cout << "  -f, stop_ext           [default:  .5] During extension, if the percentage of reads remaining after cleaning is below stop_ext, do not extend here" << endl;
  cout << "  -g, mismatch           [default:  .1] maximum percentage of mismatches allowed when fusing two contigs" << endl;
  cout << "  -x, extend_len         [default:  40] Will add a max of extend_len bp's each search loop" << endl;
  cout << "  --silent               Suppress screen output" << endl;
  cout << "  --no_log               Suppress log file creation" << endl;
  cout << "  --no_fusion            Only extend, no attempt will be made to fuse contigs" << endl;
  cout << "  --verbose              Output additional information to logfile and/or screen (except if output to that location is suppressed)" << endl;
  cout << "  --print_fused          Print to file (_fused.fasta) fused contigs just before fusion, for inspecting the fusion locations" << endl << endl;
}

// Assembly:
pushq %rbp
movq %rsp, %rbp
pushq %r15
pushq %r14
pushq %rbx
pushq %rax
movq %rdi, %r14
movq 0x18540(%rip), %rbx     # 0x1cfc0
leaq 0x105dd(%rip), %rsi     # 0x15064
movl $0x7, %edx
movq %rbx, %rdi
callq 0x4360
movq (%r14), %rsi
movq 0x8(%r14), %rdx
movq %rbx, %rdi
callq 0x4360
movq %rax, %r15
leaq 0x105bf(%rip), %rsi     # 0x1506c
movl $0x4b, %edx
movq %rax, %rdi
callq 0x4360
movq (%r15), %rax
movq -0x18(%rax), %rdi
addq %r15, %rdi
movl $0xa, %esi
callq 0x4300
movsbl %al, %esi
movq %r15, %rdi
callq 0x4030
movq %rax, %rdi
callq 0x4210
leaq 0x105d0(%rip), %rsi     # 0x150b8
movl $0x4a, %edx
movq %rbx, %rdi
callq 0x4360
movq (%rbx), %rax
movq -0x18(%rax), %rdi
addq %rbx, %rdi
movl $0xa, %esi
callq 0x4300
movsbl %al, %esi
movq %rbx, %rdi
callq 0x4030
movq %rax, %rdi
callq 0x4210
leaq 0x105e0(%rip), %rsi     # 0x15103
movl $0x57, %edx
movq %rbx, %rdi
callq 0x4360
movq (%rbx), %rax
movq -0x18(%rax), %rdi
addq %rbx, %rdi
movl $0xa, %esi
callq 0x4300
movsbl %al, %esi
movq %rbx, %rdi
callq 0x4030
movq %rax, %rdi
callq 0x4210
leaq 0x105fd(%rip), %rsi     # 0x1515b
movl $0x49, %edx
movq %rbx, %rdi
callq 0x4360
movq (%rbx), %rax
movq -0x18(%rax), %rdi
addq %rbx, %rdi
movl $0xa, %esi
callq 0x4300
movsbl %al, %esi
movq %rbx, %rdi
callq 0x4030
movq %rax, %rdi
callq 0x4210
movq %rax, %r15
movq (%rax), %rax
movq -0x18(%rax), %rdi
addq %r15, %rdi
movl $0xa, %esi
callq 0x4300
movsbl %al, %esi
movq %r15, %rdi
callq 0x4030
movq %rax, %rdi
callq 0x4210
leaq 0x105e2(%rip), %rsi     # 0x151a5
movl $0x7, %edx
movq %rbx, %rdi
callq 0x4360
movq (%r14), %rsi
movq 0x8(%r14), %rdx
movq %rbx, %rdi
callq 0x4360
movq %rax, %r14
leaq 0x105c4(%rip), %rsi     # 0x151ad
movl $0xc, %edx
movq %rax, %rdi
callq 0x4360
movq (%r14), %rax
movq -0x18(%rax), %rdi
addq %r14, %rdi
movl $0xa, %esi
callq 0x4300
movsbl %al, %esi
movq %r14, %rdi
callq 0x4030
movq %rax, %rdi
callq 0x4210
movq %rax, %r14
movq (%rax), %rax
movq -0x18(%rax), %rdi
addq %r14, %rdi
movl $0xa, %esi
callq 0x4300
movsbl %al, %esi
movq %r14, %rdi
callq 0x4030
movq %rax, %rdi
callq 0x4210
movq (%rbx), %rax
movq -0x18(%rax), %rdi
addq %rbx, %rdi
movl $0xa, %esi
callq 0x4300
movsbl %al, %esi
movq %rbx, %rdi
callq 0x4030
movq %rax, %rdi
callq 0x4210
leaq 0x10545(%rip), %rsi     # 0x151ba
movl $0x54, %edx
movq %rbx, %rdi
callq 0x4360
movq (%rbx), %rax
movq -0x18(%rax), %rdi
addq %rbx, %rdi
movl $0xa, %esi
callq 0x4300
movsbl %al, %esi
movq %rbx, %rdi
callq 0x4030
movq %rax, %rdi
callq 0x4210
leaq 0x1055f(%rip), %rsi     # 0x1520f
movl $0x52, %edx
movq %rbx, %rdi
callq 0x4360
movq (%rbx), %rax
movq -0x18(%rax), %rdi
addq %rbx, %rdi
movl $0xa, %esi
callq 0x4300
movsbl %al, %esi
movq %rbx, %rdi
callq 0x4030
movq %rax, %rdi
callq 0x4210
leaq 0x10577(%rip), %rsi     # 0x15262
movl $0x91, %edx
movq %rbx, %rdi
callq 0x4360
movq (%rbx), %rax
movq -0x18(%rax), %rdi
addq %rbx, %rdi
movl $0xa, %esi
callq 0x4300
movsbl %al, %esi
movq %rbx, %rdi
callq 0x4030
movq %rax, %rdi
callq 0x4210
leaq 0x105ce(%rip), %rsi     # 0x152f4
movl $0x5d, %edx
movq %rbx, %rdi
callq 0x4360
movq (%rbx), %rax
movq -0x18(%rax), %rdi
addq %rbx, %rdi
movl $0xa, %esi
callq 0x4300
movsbl %al, %esi
movq %rbx, %rdi
callq 0x4030
movq %rax, %rdi
callq 0x4210
leaq 0x105f1(%rip), %rsi     # 0x15352
movl $0x7d, %edx
movq %rbx, %rdi
callq 0x4360
movq (%rbx), %rax
movq -0x18(%rax), %rdi
addq %rbx, %rdi
movl $0xa, %esi
callq 0x4300
movsbl %al, %esi
movq %rbx, %rdi
callq 0x4030
movq %rax, %rdi
callq 0x4210
leaq 0x10634(%rip), %rsi     # 0x153d0
movl $0x80, %edx
movq %rbx, %rdi
callq 0x4360
movq (%rbx), %rax
movq -0x18(%rax), %rdi
addq %rbx, %rdi
movl $0xa, %esi
callq 0x4300
movsbl %al, %esi
movq %rbx, %rdi
callq 0x4030
movq %rax, %rdi
callq 0x4210
leaq 0x1067a(%rip), %rsi     # 0x15451
movl $0x63, %edx
movq %rbx, %rdi
callq 0x4360
movq (%rbx), %rax
movq -0x18(%rax), %rdi
addq %rbx, %rdi
movl $0xa, %esi
callq 0x4300
movsbl %al, %esi
movq %rbx, %rdi
callq 0x4030
movq %rax, %rdi
callq 0x4210
leaq 0x106a3(%rip), %rsi     # 0x154b5
movl $0x8c, %edx
movq %rbx, %rdi
callq 0x4360
movq (%rbx), %rax
movq -0x18(%rax), %rdi
addq %rbx, %rdi
movl $0xa, %esi
callq 0x4300
movsbl %al, %esi
movq %rbx, %rdi
callq 0x4030
movq %rax, %rdi
callq 0x4210
leaq 0x106f5(%rip), %rsi     # 0x15542
movl $0x53, %edx
movq %rbx, %rdi
callq 0x4360
movq (%rbx), %rax
movq -0x18(%rax), %rdi
addq %rbx, %rdi
movl $0xa, %esi
callq 0x4300
movsbl %al, %esi
movq %rbx, %rdi
callq 0x4030
movq %rax, %rdi
callq 0x4210
leaq 0x1070e(%rip), %rsi     # 0x15596
movl $0x7b, %edx
movq %rbx, %rdi
callq 0x4360
movq (%rbx), %rax
movq -0x18(%rax), %rdi
addq %rbx, %rdi
movl $0xa, %esi
callq 0x4300
movsbl %al, %esi
movq %rbx, %rdi
callq 0x4030
movq %rax, %rdi
callq 0x4210
leaq 0x1074f(%rip), %rsi     # 0x15612
movl $0x7d, %edx
movq %rbx, %rdi
callq 0x4360
movq (%rbx), %rax
movq -0x18(%rax), %rdi
addq %rbx, %rdi
movl $0xa, %esi
callq 0x4300
movsbl %al, %esi
movq %rbx, %rdi
callq 0x4030
movq %rax, %rdi
callq 0x4210
leaq 0x10792(%rip), %rsi     # 0x15690
movl $0x93, %edx
movq %rbx, %rdi
callq 0x4360
movq (%rbx), %rax
movq -0x18(%rax), %rdi
addq %rbx, %rdi
movl $0xa, %esi
callq 0x4300
movsbl %al, %esi
movq %rbx, %rdi
callq 0x4030
movq %rax, %rdi
callq 0x4210
leaq 0x107eb(%rip), %rsi     # 0x15724
movl $0x68, %edx
movq %rbx, %rdi
callq 0x4360
movq (%rbx), %rax
movq -0x18(%rax), %rdi
addq %rbx, %rdi
movl $0xa, %esi
callq 0x4300
movsbl %al, %esi
movq %rbx, %rdi
callq 0x4030
movq %rax, %rdi
callq 0x4210
leaq 0x10819(%rip), %rsi     # 0x1578d
movl $0x5a, %edx
movq %rbx, %rdi
callq 0x4360
movq (%rbx), %rax
movq -0x18(%rax), %rdi
addq %rbx, %rdi
movl $0xa, %esi
callq 0x4300
movsbl %al, %esi
movq %rbx, %rdi
callq 0x4030
movq %rax, %rdi
callq 0x4210
leaq 0x10839(%rip), %rsi     # 0x157e8
movl $0x2f, %edx
movq %rbx, %rdi
callq 0x4360
movq (%rbx), %rax
movq -0x18(%rax), %rdi
addq %rbx, %rdi
movl $0xa, %esi
callq 0x4300
movsbl %al, %esi
movq %rbx, %rdi
callq 0x4030
movq %rax, %rdi
callq 0x4210
leaq 0x1082e(%rip), %rsi     # 0x15818
movl $0x33, %edx
movq %rbx, %rdi
callq 0x4360
movq (%rbx), %rax
movq -0x18(%rax), %rdi
addq %rbx, %rdi
movl $0xa, %esi
callq 0x4300
movsbl %al, %esi
movq %rbx, %rdi
callq 0x4030
movq %rax, %rdi
callq 0x4210
leaq 0x10827(%rip), %rsi     # 0x1584c
movl $0x4d, %edx
movq %rbx, %rdi
callq 0x4360
movq (%rbx), %rax
movq -0x18(%rax), %rdi
addq %rbx, %rdi
movl $0xa, %esi
callq 0x4300
movsbl %al, %esi
movq %rbx, %rdi
callq 0x4030
movq %rax, %rdi
callq 0x4210
leaq 0x1083a(%rip), %rsi     # 0x1589a
movl $0x81, %edx
movq %rbx, %rdi
callq 0x4360
movq (%rbx), %rax
movq -0x18(%rax), %rdi
addq %rbx, %rdi
movl $0xa, %esi
callq 0x4300
movsbl %al, %esi
movq %rbx, %rdi
callq 0x4030
movq %rax, %rdi
callq 0x4210
leaq 0x10881(%rip), %rsi     # 0x1591c
movl $0x7b, %edx
movq %rbx, %rdi
callq 0x4360
movq (%rbx), %rax
movq -0x18(%rax), %rdi
addq %rbx, %rdi
movl $0xa, %esi
callq 0x4300
movsbl %al, %esi
movq %rbx, %rdi
callq 0x4030
movq %rax, %rdi
callq 0x4210
movq %rax, %rbx
movq (%rax), %rax
movq -0x18(%rax), %rdi
addq %rbx, %rdi
movl $0xa, %esi
callq 0x4300
movsbl %al, %esi
movq %rbx, %rdi
callq 0x4030
movq %rax, %rdi
addq $0x8, %rsp
popq %rbx
popq %r14
popq %r15
popq %rbp
jmp 0x4210