// File: /workspace/github_c_makefile_star2_O0/genometools[P]genometools/src/tools/gt_compreads_refcompress.c
// Function: gt_compreads_refcompress_option_parser_new
static GtOptionParser*
gt_compreads_refcompress_option_parser_new(void *tool_arguments)
{
  GtCsrRcrEncodeArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option,
           *option1;
  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] (-bam file -ref file)",
                         "Generates compact encoding for fastq data using"
                         " Reference Compressed Reads (RCR).");

  option = gt_option_new_bool("v", "be verbose",
                              &arguments->verbose, false);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_bool("mquals", "store mapping quality for each read",
                              &arguments->mquals, false);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_bool("quals", "store all quality values for each read,"
                                        " this implies enabling of option"
                                        " \"vquals\"",
                              &arguments->quals, false);

  option1 = gt_option_new_bool("vquals", "store quality values of read"
                               " positions having variations compared to"
                               " reference",
                              &arguments->vquals, false);

  gt_option_exclude(option, option1);

  gt_option_parser_add_option(op, option);
  gt_option_parser_add_option(op, option1);

  option = gt_option_new_bool("descs", "store read name for each read",
                              &arguments->descs, false);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_bool("ureads", "store unmapped reads in a separated"
                              " fastq file (base name will be the value given"
                              " in name and suffix will be"
                              " \" _unmapped.fastq\"",
                              &arguments->ureads, false);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_string("ref", "Index file (generated by the gt encseq"
                                " tool) for reference genome.",
                                arguments->ref, NULL);
  gt_option_is_mandatory(option);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_string("bam", "File containing alignment of reads to"
                                " genome (sorted \".bam\" file).",
                                arguments->align, NULL);
  gt_option_is_mandatory(option);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_string("name", "specify base name for RCR to be"
                                " generated. If not set, base name will be set"
                                " to base name of value given for option"
                                " \"bam\"",
                                arguments->name, NULL);
  gt_option_parser_add_option(op, option);

  gt_option_parser_set_min_max_args(op, 0U, 0U);
  return op;
}

// Assembly:
subq $0x28, %rsp
movq %rdi, 0x20(%rsp)
movq 0x20(%rsp), %rax
movq %rax, 0x18(%rsp)
cmpq $0x0, 0x18(%rsp)
jne 0x211b3
movq 0x61ae1e(%rip), %rax    # 0x63bfa0
movq (%rax), %rdi
leaq 0x4f4e87(%rip), %rsi    # 0x516013
leaq 0x5599cc(%rip), %rdx    # 0x57ab5f
leaq 0x4f7286(%rip), %rcx    # 0x518420
leaq 0x4f725a(%rip), %r8     # 0x5183fb
movl $0x50, %r9d
movb $0x0, %al
callq 0x199f0
callq 0x19370
jmp 0x211b5
leaq 0x4f728f(%rip), %rdi    # 0x51844b
leaq 0x4f72ab(%rip), %rsi    # 0x51846e
callq 0xf1420
movq %rax, 0x10(%rsp)
movq 0x18(%rsp), %rdx
leaq 0x540e4a(%rip), %rdi    # 0x562023
leaq 0x4f6f44(%rip), %rsi    # 0x518124
xorl %ecx, %ecx
callq 0xf5f20
movq %rax, 0x8(%rsp)
movq 0x10(%rsp), %rdi
movq 0x8(%rsp), %rsi
callq 0xf1600
movq 0x18(%rsp), %rdx
addq $0x2, %rdx
leaq 0x4f72b5(%rip), %rdi    # 0x5184c0
leaq 0x4f72b5(%rip), %rsi    # 0x5184c7
xorl %ecx, %ecx
callq 0xf5f20
movq %rax, 0x8(%rsp)
movq 0x10(%rsp), %rdi
movq 0x8(%rsp), %rsi
callq 0xf1600
movq 0x18(%rsp), %rdx
addq $0x3, %rdx
leaq 0x5402e6(%rip), %rdi    # 0x561523
leaq 0x4f72a7(%rip), %rsi    # 0x5184eb
xorl %ecx, %ecx
callq 0xf5f20
movq %rax, 0x8(%rsp)
movq 0x18(%rsp), %rdx
addq $0x1, %rdx
leaq 0x5402bb(%rip), %rdi    # 0x56151b
leaq 0x4f72d5(%rip), %rsi    # 0x51853c
xorl %ecx, %ecx
callq 0xf5f20
movq %rax, (%rsp)
movq 0x8(%rsp), %rdi
movq (%rsp), %rsi
callq 0xf7320
movq 0x10(%rsp), %rdi
movq 0x8(%rsp), %rsi
callq 0xf1600
movq 0x10(%rsp), %rdi
movq (%rsp), %rsi
callq 0xf1600
movq 0x18(%rsp), %rdx
addq $0x5, %rdx
leaq 0x564375(%rip), %rdi    # 0x585622
leaq 0x4f72d7(%rip), %rsi    # 0x51858b
xorl %ecx, %ecx
callq 0xf5f20
movq %rax, 0x8(%rsp)
movq 0x10(%rsp), %rdi
movq 0x8(%rsp), %rsi
callq 0xf1600
movq 0x18(%rsp), %rdx
addq $0x4, %rdx
leaq 0x4f72ca(%rip), %rdi    # 0x5185a9
leaq 0x4f72ca(%rip), %rsi    # 0x5185b0
xorl %ecx, %ecx
callq 0xf5f20
movq %rax, 0x8(%rsp)
movq 0x10(%rsp), %rdi
movq 0x8(%rsp), %rsi
callq 0xf1600
movq 0x18(%rsp), %rax
movq 0x10(%rax), %rdx
leaq 0x527fcc(%rip), %rdi    # 0x5492dd
leaq 0x4f7318(%rip), %rsi    # 0x518630
xorl %eax, %eax
movl %eax, %ecx
callq 0xf69f0
movq %rax, 0x8(%rsp)
movq 0x8(%rsp), %rdi
callq 0xf6ca0
movq 0x10(%rsp), %rdi
movq 0x8(%rsp), %rsi
callq 0xf1600
movq 0x18(%rsp), %rax
movq 0x18(%rax), %rdx
leaq 0x505976(%rip), %rdi    # 0x526cc5
leaq 0x4f731d(%rip), %rsi    # 0x518673
xorl %eax, %eax
movl %eax, %ecx
callq 0xf69f0
movq %rax, 0x8(%rsp)
movq 0x8(%rsp), %rdi
callq 0xf6ca0
movq 0x10(%rsp), %rdi
movq 0x8(%rsp), %rsi
callq 0xf1600
movq 0x18(%rsp), %rax
movq 0x8(%rax), %rdx
leaq 0x533a71(%rip), %rdi    # 0x554dfe
leaq 0x4f7322(%rip), %rsi    # 0x5186b6
xorl %eax, %eax
movl %eax, %ecx
callq 0xf69f0
movq %rax, 0x8(%rsp)
movq 0x10(%rsp), %rdi
movq 0x8(%rsp), %rsi
callq 0xf1600
movq 0x10(%rsp), %rdi
xorl %edx, %edx
movl %edx, %esi
callq 0xf2a40
movq 0x10(%rsp), %rax
addq $0x28, %rsp
retq
nopl (%rax)