// File: /workspace/github_c_makefile_star2_O2/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:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0x1cb60
movq %rdi, %r14
leaq 0x2caa45(%rip), %rdi    # 0x2e7411
leaq 0x2caa61(%rip), %rsi    # 0x2e7434
callq 0x97df5
movq %rax, %rbx
leaq 0x31318e(%rip), %rdi    # 0x32fb70
leaq 0x2ca701(%rip), %rsi    # 0x2e70ea
movq %r14, %rdx
xorl %ecx, %ecx
callq 0x9a997
movq %rbx, %rdi
movq %rax, %rsi
callq 0x97f31
leaq 0x2(%r14), %rdx
leaq 0x2caa7d(%rip), %rdi    # 0x2e7486
leaq 0x2caa7d(%rip), %rsi    # 0x2e748d
xorl %ecx, %ecx
callq 0x9a997
movq %rbx, %rdi
movq %rax, %rsi
callq 0x97f31
leaq 0x3(%r14), %rdx
leaq 0x369e28(%rip), %rdi    # 0x386855
leaq 0x2caa7d(%rip), %rsi    # 0x2e74b1
xorl %ecx, %ecx
callq 0x9a997
movq %rax, %r15
leaq 0x1(%r14), %rdx
leaq 0x312626(%rip), %rdi    # 0x32f06f
leaq 0x2caab2(%rip), %rsi    # 0x2e7502
xorl %ecx, %ecx
callq 0x9a997
movq %rax, %r12
movq %r15, %rdi
movq %rax, %rsi
callq 0x9b38d
movq %rbx, %rdi
movq %r15, %rsi
callq 0x97f31
movq %rbx, %rdi
movq %r12, %rsi
callq 0x97f31
leaq 0x5(%r14), %rdx
leaq 0x33623e(%rip), %rdi    # 0x352cc4
leaq 0x2caac4(%rip), %rsi    # 0x2e7551
xorl %ecx, %ecx
callq 0x9a997
movq %rbx, %rdi
movq %rax, %rsi
callq 0x97f31
leaq 0x4(%r14), %rdx
leaq 0x2caac5(%rip), %rdi    # 0x2e756f
leaq 0x2caac5(%rip), %rsi    # 0x2e7576
xorl %ecx, %ecx
callq 0x9a997
movq %rbx, %rdi
movq %rax, %rsi
callq 0x97f31
movq 0x10(%r14), %rdx
leaq 0x2fa87a(%rip), %rdi    # 0x317348
leaq 0x2cab21(%rip), %rsi    # 0x2e75f6
xorl %ecx, %ecx
callq 0x9ad12
movq %rax, %r15
movq %rax, %rdi
callq 0x9ae37
movq %rbx, %rdi
movq %r15, %rsi
callq 0x97f31
movq 0x18(%r14), %rdx
leaq 0x2d911c(%rip), %rdi    # 0x2f5c19
leaq 0x2cab35(%rip), %rsi    # 0x2e7639
xorl %ecx, %ecx
callq 0x9ad12
movq %rax, %r15
movq %rax, %rdi
callq 0x9ae37
movq %rbx, %rdi
movq %r15, %rsi
callq 0x97f31
movq 0x8(%r14), %rdx
leaq 0x30603f(%rip), %rdi    # 0x322b6b
leaq 0x2cab49(%rip), %rsi    # 0x2e767c
xorl %ecx, %ecx
callq 0x9ad12
movq %rbx, %rdi
movq %rax, %rsi
callq 0x97f31
movq %rbx, %rdi
xorl %esi, %esi
xorl %edx, %edx
callq 0x98c6b
movq %rbx, %rax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
movq 0x41b401(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x2c84a2(%rip), %rsi    # 0x2e5013
leaq 0x32badb(%rip), %rdx    # 0x348653
leaq 0x2ca867(%rip), %rcx    # 0x2e73e6
leaq 0x2ca83b(%rip), %r8     # 0x2e73c1
pushq $0x50
popq %r9
xorl %eax, %eax
callq 0x17a50
callq 0x17390