LLM4Binary/decompile-bench-makefile huggingface dataset:
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/core/seq_iterator_sequence_buffer.c
// Function: gt_seq_iterator_sequence_buffer_set_symbolmap
static void gt_seq_iterator_sequence_buffer_set_symbolmap(GtSeqIterator *si,
                                                         const GtUchar
                                                           *symbolmap)
{
  GtSeqIteratorSequenceBuffer *seqit;
  gt_assert(si);
  seqit = gt_seq_iterator_sequence_buffer_cast(si);
  gt_sequence_buffer_set_symbolmap(seqit->fb, symbolmap);
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0xa7201
movq %rsi, %rbx
movq %rdi, %r14
callq 0xa7178
movq %rax, %rdi
movq %r14, %rsi
callq 0xa615e
movq 0x8(%rax), %rdi
movq %rbx, %rsi
addq $0x8, %rsp
popq %rbx
popq %r14
jmp 0xa7a10
movq 0x390d60(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x23de01(%rip), %rsi    # 0x2e5013
leaq 0x26919b(%rip), %rdx    # 0x3103b4
leaq 0x269820(%rip), %rcx    # 0x310a40
leaq 0x269847(%rip), %r8     # 0x310a6e
pushq $0x54
popq %r9
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/core/seq_iterator_sequence_buffer.c
// Function: gt_seq_iterator_sequence_buffer_set_sequence_output
static void gt_seq_iterator_sequence_buffer_set_sequence_output(
                                                          GtSeqIterator *si,
                                                          bool withsequence)
{
  GtSeqIteratorSequenceBuffer *seqit;
  gt_assert(si);
  seqit = gt_seq_iterator_sequence_buffer_cast(si);
  seqit->withsequence = withsequence;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0xa7260
movl %esi, %ebx
movq %rdi, %r14
callq 0xa7178
movq %rax, %rdi
movq %r14, %rsi
callq 0xa615e
movb %bl, 0x48(%rax)
addq $0x8, %rsp
popq %rbx
popq %r14
retq
movq 0x390d01(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x23dda2(%rip), %rsi    # 0x2e5013
leaq 0x26913c(%rip), %rdx    # 0x3103b4
leaq 0x269817(%rip), %rcx    # 0x310a96
leaq 0x2697e8(%rip), %r8     # 0x310a6e
pushq $0x5e
popq %r9
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/core/seq_iterator_sequence_buffer.c
// Function: gt_seq_iterator_sequence_buffer_getcurrentcounter
static const GtUint64*
gt_seq_iterator_sequence_buffer_getcurrentcounter(GtSeqIterator *si,
                                                 GtUint64 maxread)
{
  GtSeqIteratorSequenceBuffer *seqit;
  gt_assert(si);
  seqit = gt_seq_iterator_sequence_buffer_cast(si);
  seqit->maxread = maxread;
  return &seqit->currentread;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0xa75a1
movq %rsi, %rbx
movq %rdi, %r14
callq 0xa7178
movq %rax, %rdi
movq %r14, %rsi
callq 0xa615e
movq %rbx, 0x58(%rax)
addq $0x50, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
movq 0x3909c0(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x23da61(%rip), %rsi    # 0x2e5013
leaq 0x268dfb(%rip), %rdx    # 0x3103b4
leaq 0x2695af(%rip), %rcx    # 0x310b6f
leaq 0x2694a7(%rip), %r8     # 0x310a6e
movl $0xc6, %r9d
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/core/seq_iterator_sequence_buffer.c
// Function: gt_seq_iterator_sequence_buffer_delete
static void gt_seq_iterator_sequence_buffer_delete(GtSeqIterator *si)
{
  GtSeqIteratorSequenceBuffer *seqit;
  if (!si) return;
  seqit = gt_seq_iterator_sequence_buffer_cast(si);
  gt_desc_buffer_delete(seqit->descptr);
  gt_sequence_buffer_delete(seqit->fb);
  GT_FREEARRAY(&seqit->sequencebuffer, GtUchar);
  seqit->currentread = seqit->maxread;
}

// Assembly:
testq %rdi, %rdi
je 0xa7646
pushq %r14
pushq %rbx
pushq %rax
movq %rdi, %rbx
callq 0xa7178
movq %rax, %rdi
movq %rbx, %rsi
callq 0xa615e
movq %rax, %rbx
movq 0x20(%rax), %rdi
callq 0x6d2bb
movq 0x8(%rbx), %rdi
callq 0xa76dc
movq 0x28(%rbx), %rdi
testq %rdi, %rdi
je 0xa7637
movq %rbx, %r14
addq $0x28, %r14
leaq 0x26944d(%rip), %rsi    # 0x310a6e
movl $0xd3, %edx
callq 0x936f9
xorps %xmm0, %xmm0
movups %xmm0, (%r14)
andq $0x0, 0x10(%r14)
movq 0x58(%rbx), %rax
movq %rax, 0x50(%rbx)
addq $0x8, %rsp
popq %rbx
popq %r14
retq
nop
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/core/tool.c
// Function: gt_tool_new
GtTool* gt_tool_new(GtToolArgumentsNew tool_arguments_new,
                    GtToolArgumentsDelete tool_arguments_delete,
                    GtToolOptionParserNew tool_option_parser_new,
                    GtToolArgumentsCheck tool_arguments_check,
                    GtToolRunner tool_runner)
{
  GtTool *tool;
  gt_assert(tool_option_parser_new && tool_runner); /* required arguments */
  /* <tool_arguments_new> and <tool_arguments_delete> imply each other */
  gt_assert(( tool_arguments_new &&  tool_arguments_delete) ||
         (!tool_arguments_new && !tool_arguments_delete));
  tool = gt_calloc(1, sizeof *tool);
  tool->tool_arguments_new = tool_arguments_new;
  tool->tool_arguments_delete = tool_arguments_delete;
  tool->tool_option_parser_new = tool_option_parser_new;
  tool->tool_arguments_check = tool_arguments_check;
  tool->tool_runner = tool_runner;
  return tool;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
testq %rdx, %rdx
je 0xb0534
movq %r8, %rbx
testq %r8, %r8
je 0xb0534
movq %rcx, %r14
movq %rsi, %r12
movq %rdi, %r13
testq %rdi, %rdi
setne %al
testq %rsi, %rsi
setne %cl
cmpb %cl, %al
jne 0xb055e
movq %rdx, %r15
leaq 0x26230f(%rip), %rdx    # 0x312818
pushq $0x1
popq %rdi
pushq $0x50
popq %rsi
pushq $0x2e
popq %rcx
callq 0x9334a
movq %r13, (%rax)
movq %r12, 0x8(%rax)
movq %r15, 0x10(%rax)
movq %r14, 0x18(%rax)
movq %rbx, 0x20(%rax)
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
retq
movq 0x387a2d(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x234ace(%rip), %rsi    # 0x2e5013
leaq 0x26229a(%rip), %rdx    # 0x3127e6
leaq 0x2622b9(%rip), %rcx    # 0x31280c
leaq 0x2622be(%rip), %r8     # 0x312818
pushq $0x2a
jmp 0xb0586
movq 0x387a03(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x234aa4(%rip), %rsi    # 0x2e5013
leaq 0x2622b2(%rip), %rdx    # 0x312828
leaq 0x26228f(%rip), %rcx    # 0x31280c
leaq 0x262294(%rip), %r8     # 0x312818
pushq $0x2d
popq %r9
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/core/tool.c
// Function: gt_tool_get_toolbox
GtToolbox* gt_tool_get_toolbox(GtTool *tool)
{
  gt_assert(tool && tool->tool_toolbox_new);
  if (!tool->toolbox)
    tool->toolbox = tool->tool_toolbox_new();
  return tool->toolbox;
}

// Assembly:
pushq %rbx
testq %rdi, %rdi
je 0xb07ab
movq %rdi, %rbx
movq 0x28(%rdi), %rcx
testq %rcx, %rcx
je 0xb07ab
movq 0x40(%rbx), %rax
testq %rax, %rax
jne 0xb07a9
callq *%rcx
movq %rax, 0x40(%rbx)
popq %rbx
retq
movq 0x3877b6(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x234857(%rip), %rsi    # 0x2e5013
leaq 0x2620fe(%rip), %rdx    # 0x3128c1
leaq 0x262116(%rip), %rcx    # 0x3128e0
leaq 0x262047(%rip), %r8     # 0x312818
movl $0x81, %r9d
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/core/tool.c
// Function: gt_tool_get_option_parser
GtOptionParser* gt_tool_get_option_parser(GtTool *tool)
{
  gt_assert(tool && tool->tool_option_parser_new);
  if (tool->tool_arguments_new && !tool->arguments)
    tool->arguments = tool->tool_arguments_new();
  if (tool->tool_option_parser_new && !tool->op)
    tool->op = tool->tool_option_parser_new(tool->arguments);
  return tool->op;
}

// Assembly:
pushq %rbx
testq %rdi, %rdi
je 0xb082e
movq %rdi, %rbx
movq 0x10(%rdi), %rcx
testq %rcx, %rcx
je 0xb082e
movq (%rbx), %rax
testq %rax, %rax
je 0xb0813
cmpq $0x0, 0x30(%rbx)
jne 0xb0813
callq *%rax
movq %rax, 0x30(%rbx)
movq 0x10(%rbx), %rcx
testq %rcx, %rcx
je 0xb0828
movq 0x38(%rbx), %rax
testq %rax, %rax
jne 0xb082c
movq 0x30(%rbx), %rdi
callq *%rcx
movq %rax, 0x38(%rbx)
jmp 0xb082c
movq 0x38(%rbx), %rax
popq %rbx
retq
movq 0x387733(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x2347d4(%rip), %rsi    # 0x2e5013
leaq 0x2620ae(%rip), %rdx    # 0x3128f4
leaq 0x2620cc(%rip), %rcx    # 0x312919
leaq 0x261fc4(%rip), %r8     # 0x312818
movl $0x89, %r9d
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/core/tool.c
// Function: gt_tool_delete
void gt_tool_delete(GtTool *tool)
{
  if (!tool) return;
  if (tool->reference_count) {
    tool->reference_count--;
    return;
  }
  if (tool->arguments && tool->tool_arguments_delete)
    tool->tool_arguments_delete(tool->arguments);
  gt_toolbox_delete(tool->toolbox);
  gt_option_parser_delete(tool->op);
  gt_free(tool);
}

// Assembly:
pushq %rbx
testq %rdi, %rdi
je 0xb087f
movq %rdi, %rbx
movq 0x48(%rdi), %rax
testq %rax, %rax
je 0xb0881
decq %rax
movq %rax, 0x48(%rbx)
popq %rbx
retq
movq 0x30(%rbx), %rdi
testq %rdi, %rdi
je 0xb0895
movq 0x8(%rbx), %rax
testq %rax, %rax
je 0xb0895
callq *%rax
movq 0x40(%rbx), %rdi
callq 0xb1193
movq 0x38(%rbx), %rdi
callq 0x9a844
leaq 0x261f6a(%rip), %rsi    # 0x312818
movq %rbx, %rdi
movl $0x9c, %edx
popq %rbx
jmp 0x936f9
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/core/tool_iterator.c
// Function: gt_tool_iterator_new
GtToolIterator* gt_tool_iterator_new(GtToolbox *toolbox)
{
  GtToolIterator *ti;
  ToolIterationInfo tii;
  gt_assert(toolbox);
  ti = gt_malloc(sizeof *ti);
  ti->tool_stack = gt_array_new(sizeof (ToolEntry));
  ti->prefixptr = NULL;
  ti->prefixsep = ' ';
  tii.arr = ti->tool_stack;
  tii.str = NULL;
  gt_toolbox_iterate(toolbox, add_tool_to_stack, &tii);
  gt_array_reverse(ti->tool_stack); /* alphabetical order */
  return ti;
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
subq $0x10, %rsp
testq %rdi, %rdi
je 0xb092a
movq %rdi, %rbx
leaq 0x262074(%rip), %rsi    # 0x312948
pushq $0x18
popq %r14
pushq $0x38
popq %rdx
movq %r14, %rdi
callq 0x93160
movq %rax, %r15
movq %r14, %rdi
callq 0x5809c
movq %rax, (%r15)
andq $0x0, 0x8(%r15)
movb $0x20, 0x10(%r15)
movq %rsp, %rdx
movq %rax, (%rdx)
andq $0x0, 0x8(%rdx)
leaq 0x53(%rip), %rsi        # 0xb0960
movq %rbx, %rdi
callq 0xb102e
movq (%r15), %rdi
callq 0x583f9
movq %r15, %rax
addq $0x10, %rsp
popq %rbx
popq %r14
popq %r15
retq
movq 0x387637(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x2346d8(%rip), %rsi    # 0x2e5013
leaq 0x24d397(%rip), %rdx    # 0x2fdcd9
leaq 0x261fea(%rip), %rcx    # 0x312933
leaq 0x261ff8(%rip), %r8     # 0x312948
pushq $0x37
popq %r9
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/core/tool_iterator.c
// Function: add_tool_to_stack
static void add_tool_to_stack(const char *name, GtTool *tool, void *data)
{
  ToolIterationInfo *ti_info = data;
  ToolEntry entry;
  gt_assert(name && tool && data);
  entry.name = name;
  entry.tool = tool;
  entry.prefix = gt_str_ref(ti_info->str);
  gt_array_add(ti_info->arr, entry);
}

// Assembly:
pushq %r14
pushq %rbx
subq $0x18, %rsp
testq %rdi, %rdi
je 0xb09a6
testq %rsi, %rsi
je 0xb09a6
movq %rdx, %rbx
testq %rdx, %rdx
je 0xb09a6
movq %rsp, %r14
movq %rdi, (%r14)
movq %rsi, 0x8(%r14)
movq 0x8(%rbx), %rdi
callq 0xad4d2
movq %rax, 0x10(%r14)
movq (%rbx), %rdi
pushq $0x18
popq %rdx
movq %r14, %rsi
callq 0x5851d
addq $0x18, %rsp
popq %rbx
popq %r14
retq
movq 0x3875bb(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x23465c(%rip), %rsi    # 0x2e5013
leaq 0x261ffa(%rip), %rdx    # 0x3129b8
leaq 0x262008(%rip), %rcx    # 0x3129cd
leaq 0x261f7c(%rip), %r8     # 0x312948
pushq $0x2c
popq %r9
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/core/tool_iterator.c
// Function: gt_tool_iterator_set_prefix_target
void gt_tool_iterator_set_prefix_target(GtToolIterator *ti, GtStr *prefix,
                                        char sep)
{
  gt_assert(ti);
  if (ti->prefixptr)
    gt_str_delete(ti->prefixptr);
  ti->prefixptr = gt_str_ref(prefix);
  ti->prefixsep = sep;
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
testq %rdi, %rdi
je 0xb0a12
movl %edx, %ebx
movq %rsi, %r15
movq %rdi, %r14
movq 0x8(%rdi), %rdi
testq %rdi, %rdi
je 0xb09fc
callq 0xae103
movq %r15, %rdi
callq 0xad4d2
movq %rax, 0x8(%r14)
movb %bl, 0x10(%r14)
popq %rbx
popq %r14
popq %r15
retq
movq 0x38754f(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x2345f0(%rip), %rsi    # 0x2e5013
leaq 0x252543(%rip), %rdx    # 0x302f6d
leaq 0x261f30(%rip), %rcx    # 0x312961
leaq 0x261f10(%rip), %r8     # 0x312948
pushq $0x46
popq %r9
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/core/tool_iterator.c
// Function: gt_tool_iterator_delete
void gt_tool_iterator_delete(GtToolIterator *tool_iterator)
{
  if (!tool_iterator) return;
  gt_array_delete(tool_iterator->tool_stack);
  gt_str_delete(tool_iterator->prefixptr);
  gt_free(tool_iterator);
}

// Assembly:
testq %rdi, %rdi
je 0xb0bea
pushq %rbx
movq %rdi, %rbx
movq (%rdi), %rdi
callq 0x58eb9
movq 0x8(%rbx), %rdi
callq 0xae103
leaq 0x261d6a(%rip), %rsi    # 0x312948
pushq $0x7c
popq %rdx
movq %rbx, %rdi
popq %rbx
jmp 0x936f9
retq
nop
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/core/toolbox.c
// Function: gt_toolbox_add_tool
void gt_toolbox_add_tool(GtToolbox *tb, const char *toolname, GtTool *tool)
{
  GtToolinfo *toolinfo;
  gt_assert(tb && tb->tools);
  toolinfo = gt_toolinfo_new();
  toolinfo->tool= tool;
  gt_hashmap_add(tb->tools, (char*) toolname, toolinfo);
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
testq %rdi, %rdi
je 0xb0c89
movq %rdi, %r15
cmpq $0x0, (%rdi)
je 0xb0c89
movq %rdx, %r14
movq %rsi, %rbx
callq 0xb0bec
movq %r14, (%rax)
movq (%r15), %rdi
movq %rbx, %rsi
movq %rax, %rdx
popq %rbx
popq %r14
popq %r15
jmp 0x8f4bd
movq 0x3872d8(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x234379(%rip), %rsi    # 0x2e5013
leaq 0x261d51(%rip), %rdx    # 0x3129f2
leaq 0x261d5a(%rip), %rcx    # 0x312a02
leaq 0x261d30(%rip), %r8     # 0x3129df
pushq $0x3b
popq %r9
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/core/toolbox.c
// Function: gt_toolbox_add_hidden_tool
void gt_toolbox_add_hidden_tool(GtToolbox *tb, const char *toolname,
                                GtTool *tool)
{
  GtToolinfo *toolinfo;
  gt_assert(tb && tb->tools);
  toolinfo = gt_toolinfo_new();
  toolinfo->tool= tool;
  toolinfo->hidden = true;
  gt_hashmap_add(tb->tools, (char*) toolname, toolinfo);
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
testq %rdi, %rdi
je 0xb0cf7
movq %rdi, %r14
cmpq $0x0, (%rdi)
je 0xb0cf7
movq %rdx, %r15
movq %rsi, %rbx
callq 0xb0bec
movq %r15, (%rax)
movb $0x1, 0x10(%rax)
movq (%r14), %rdi
movq %rbx, %rsi
movq %rax, %rdx
popq %rbx
popq %r14
popq %r15
jmp 0x8f4bd
movq 0x38726a(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x23430b(%rip), %rsi    # 0x2e5013
leaq 0x261ce3(%rip), %rdx    # 0x3129f2
leaq 0x261d00(%rip), %rcx    # 0x312a16
leaq 0x261cc2(%rip), %r8     # 0x3129df
pushq $0x45
popq %r9
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/core/toolbox.c
// Function: gt_toolbox_get_tool
GtTool* gt_toolbox_get_tool(GtToolbox *tb, const char *toolname)
{
  GtToolinfo *toolinfo;
  gt_assert(tb && tb->tools);
  toolinfo = gt_hashmap_get(tb->tools, toolname);
  if (toolinfo)
    return toolinfo->tool;
  return NULL;
}

// Assembly:
pushq %rax
testq %rdi, %rdi
je 0xb0d4e
movq (%rdi), %rdi
testq %rdi, %rdi
je 0xb0d4e
callq 0x8f482
testq %rax, %rax
je 0xb0d4a
movq (%rax), %rax
jmp 0xb0d4c
xorl %eax, %eax
popq %rcx
retq
movq 0x387213(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x2342b4(%rip), %rsi    # 0x2e5013
leaq 0x261c8c(%rip), %rdx    # 0x3129f2
leaq 0x261cc4(%rip), %rcx    # 0x312a31
leaq 0x261c6b(%rip), %r8     # 0x3129df
pushq $0x4f
popq %r9
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/core/toolbox.c
// Function: gt_toolbox_add
void gt_toolbox_add(GtToolbox *tb, const char *toolname, GtToolfunc toolfunc)
{
  GtToolinfo *toolinfo;
  gt_assert(tb && tb->tools);
  toolinfo = gt_toolinfo_new();
  toolinfo->toolfunc = toolfunc;
  gt_hashmap_add(tb->tools, (char*) toolname, toolinfo);
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
testq %rdi, %rdi
je 0xb0e0a
movq %rdi, %r15
cmpq $0x0, (%rdi)
je 0xb0e0a
movq %rdx, %r14
movq %rsi, %rbx
callq 0xb0bec
movq %r14, 0x8(%rax)
movq (%r15), %rdi
movq %rbx, %rsi
movq %rax, %rdx
popq %rbx
popq %r14
popq %r15
jmp 0x8f4bd
movq 0x387157(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x2341f8(%rip), %rsi    # 0x2e5013
leaq 0x261bd0(%rip), %rdx    # 0x3129f2
leaq 0x261c30(%rip), %rcx    # 0x312a59
leaq 0x261baf(%rip), %r8     # 0x3129df
pushq $0x61
popq %r9
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/core/toolbox.c
// Function: gt_toolbox_get
GtToolfunc gt_toolbox_get(const GtToolbox *tb, const char *toolname)
{
  GtToolinfo *toolinfo;
  gt_assert(tb && tb->tools);
  toolinfo = gt_hashmap_get(tb->tools, toolname);
  if (toolinfo)
    return toolinfo->toolfunc;
  return NULL;
}

// Assembly:
pushq %rax
testq %rdi, %rdi
je 0xb0e62
movq (%rdi), %rdi
testq %rdi, %rdi
je 0xb0e62
callq 0x8f482
testq %rax, %rax
je 0xb0e5e
movq 0x8(%rax), %rax
jmp 0xb0e60
xorl %eax, %eax
popq %rcx
retq
movq 0x3870ff(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x2341a0(%rip), %rsi    # 0x2e5013
leaq 0x261b78(%rip), %rdx    # 0x3129f2
leaq 0x261be7(%rip), %rcx    # 0x312a68
leaq 0x261b57(%rip), %r8     # 0x3129df
pushq $0x6a
popq %r9
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/core/toolbox.c
// Function: gt_toolbox_show
int gt_toolbox_show(GT_UNUSED const char *progname, void *toolbox,
                    GT_UNUSED GtError *err)
{
  GtToolbox *tb;
  GT_UNUSED int had_err = 0;
  gt_error_check(err);
  gt_assert(toolbox);
  tb = (GtToolbox*) toolbox;
  printf("\nTools:\n\n");
  had_err = gt_hashmap_foreach_in_key_order(tb->tools, show_tool_name, NULL,
                                            NULL);
  gt_assert(!had_err); /* show_tool_name() is sane */
  return 0;
}

// Assembly:
pushq %rbx
movq %rsi, %rbx
testq %rdx, %rdx
je 0xb0eb1
movq %rdx, %rdi
callq 0x89eb7
testb %al, %al
jne 0xb0f39
testq %rbx, %rbx
je 0xb0edd
leaq 0x261c34(%rip), %rdi    # 0x312af1
callq 0x17b60
movq (%rbx), %rdi
leaq 0xa5(%rip), %rsi        # 0xb0f71
xorl %edx, %edx
xorl %ecx, %ecx
callq 0x8f595
testl %eax, %eax
jne 0xb0f0b
xorl %eax, %eax
popq %rbx
retq
movq 0x387084(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x234125(%rip), %rsi    # 0x2e5013
leaq 0x24cde4(%rip), %rdx    # 0x2fdcd9
leaq 0x261b7b(%rip), %rcx    # 0x312a77
leaq 0x261adc(%rip), %r8     # 0x3129df
movl $0x88, %r9d
jmp 0xb0f65
movq 0x387056(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x2340f7(%rip), %rsi    # 0x2e5013
leaq 0x23475c(%rip), %rdx    # 0x2e567f
leaq 0x261b4d(%rip), %rcx    # 0x312a77
leaq 0x261aae(%rip), %r8     # 0x3129df
movl $0x8d, %r9d
jmp 0xb0f65
movq 0x387028(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x2340c9(%rip), %rsi    # 0x2e5013
leaq 0x23426e(%rip), %rdx    # 0x2e51bf
leaq 0x261b1f(%rip), %rcx    # 0x312a77
leaq 0x261a80(%rip), %r8     # 0x3129df
movl $0x87, %r9d
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/core/toolbox.c
// Function: show_tool_name
static int show_tool_name(void *key, void *value, GT_UNUSED void *data,
                          GT_UNUSED GtError *err)
{
  GtToolinfo *toolinfo = value;
  gt_error_check(err);
  gt_assert(key && value);
  if (!toolinfo->hidden) {
    if (gt_createman)
      printf("- *%s*\n", (const char*) key);
    else
      gt_xputs(key);
  }
  return 0;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rsi, %r14
movq %rdi, %rbx
testq %rcx, %rcx
je 0xb0f8c
movq %rcx, %rdi
callq 0x89eb7
testb %al, %al
jne 0xb0ff8
testq %rbx, %rbx
je 0xb0fce
testq %r14, %r14
je 0xb0fce
cmpb $0x0, 0x10(%r14)
jne 0xb0fc4
leaq 0x38c58c(%rip), %rax    # 0x43d530
cmpb $0x1, (%rax)
jne 0xb0fbc
leaq 0x261b04(%rip), %rdi    # 0x312ab4
movq %rbx, %rsi
xorl %eax, %eax
callq 0x17070
jmp 0xb0fc4
movq %rbx, %rdi
callq 0xb30e8
xorl %eax, %eax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
movq 0x386f93(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x234034(%rip), %rsi    # 0x2e5013
leaq 0x2b5680(%rip), %rdx    # 0x366666
leaq 0x261ab8(%rip), %rcx    # 0x312aa5
leaq 0x2619eb(%rip), %r8     # 0x3129df
pushq $0x78
jmp 0xb1020
movq 0x386f69(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x23400a(%rip), %rsi    # 0x2e5013
leaq 0x2341af(%rip), %rdx    # 0x2e51bf
leaq 0x261a8e(%rip), %rcx    # 0x312aa5
leaq 0x2619c1(%rip), %r8     # 0x3129df
pushq $0x77
popq %r9
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/core/toolbox.c
// Function: gt_toolbox_iterate
void gt_toolbox_iterate(const GtToolbox *tb, GtToolboxIterator func, void *data)
{
  IterateInfo info;
  GT_UNUSED int had_err = 0;
  gt_assert(tb && func);
  info.func = func;
  info.data = data;
  had_err = gt_hashmap_foreach_in_key_order(tb->tools, toolbox_iterate, &info,
                                            NULL);
  gt_assert(!had_err); /* func() is sane */
}

// Assembly:
subq $0x18, %rsp
testq %rdi, %rdi
je 0xb1065
testq %rsi, %rsi
je 0xb1065
leaq 0x8(%rsp), %rax
movq %rsi, (%rax)
movq %rdx, 0x8(%rax)
movq (%rdi), %rdi
leaq 0x79(%rip), %rsi        # 0xb10cb
movq %rax, %rdx
xorl %ecx, %ecx
callq 0x8f595
testl %eax, %eax
jne 0xb1093
addq $0x18, %rsp
retq
movq 0x386efc(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x233f9d(%rip), %rsi    # 0x2e5013
leaq 0x261a0a(%rip), %rdx    # 0x312a87
leaq 0x261a0e(%rip), %rcx    # 0x312a92
leaq 0x261954(%rip), %r8     # 0x3129df
movl $0xab, %r9d
jmp 0xb10bf
movq 0x386ece(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x233f6f(%rip), %rsi    # 0x2e5013
leaq 0x2345d4(%rip), %rdx    # 0x2e567f
leaq 0x2619e0(%rip), %rcx    # 0x312a92
leaq 0x261926(%rip), %r8     # 0x3129df
movl $0xb0, %r9d
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/core/toolbox.c
// Function: toolbox_iterate
static int toolbox_iterate(void *key, void *value, void *data,
                           GT_UNUSED GtError *err)
{
  const char *name = key;
  GtToolinfo *toolinfo = value;
  IterateInfo *info = data;
  gt_error_check(err);
  gt_assert(key && value && data);
  if (!toolinfo->hidden) {
    if (toolinfo->tool)
      info->func(name, toolinfo->tool, info->data);
    else
      gt_warning("skipping tool '%s' in iterator (not a GtTool object)", name);
  }
  return 0;
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
movq %rdx, %r14
movq %rsi, %r15
movq %rdi, %rbx
testq %rcx, %rcx
je 0xb10ea
movq %rcx, %rdi
callq 0x89eb7
testb %al, %al
jne 0xb115b
testq %rbx, %rbx
je 0xb112d
testq %r15, %r15
je 0xb112d
testq %r14, %r14
je 0xb112d
cmpb $0x0, 0x10(%r15)
jne 0xb1125
movq (%r15), %rsi
testq %rsi, %rsi
je 0xb1114
movq 0x8(%r14), %rdx
movq %rbx, %rdi
callq *(%r14)
jmp 0xb1125
leaq 0x2619a1(%rip), %rdi    # 0x312abc
movq %rbx, %rsi
xorl %eax, %eax
callq 0xb2cd0
xorl %eax, %eax
popq %rbx
popq %r14
popq %r15
retq
movq 0x386e34(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x233ed5(%rip), %rsi    # 0x2e5013
leaq 0x25922b(%rip), %rdx    # 0x30a370
leaq 0x261949(%rip), %rcx    # 0x312a95
leaq 0x26188c(%rip), %r8     # 0x3129df
movl $0x9d, %r9d
jmp 0xb1187
movq 0x386e06(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x233ea7(%rip), %rsi    # 0x2e5013
leaq 0x23404c(%rip), %rdx    # 0x2e51bf
leaq 0x26191b(%rip), %rcx    # 0x312a95
leaq 0x26185e(%rip), %r8     # 0x3129df
movl $0x9c, %r9d
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/core/unit_testing.c
// Function: gt_unit_test_run
int gt_unit_test_run(void *key, void *value, void *data, GtError *err)
{
  int had_err, *had_errp;
  char *testname = key;
  GtUnitTestFunc test = value;
  gt_error_check(err);
  gt_assert(testname && test && data);
  had_errp = (int*) data;
  printf("%s...", testname);
  gt_xfflush(stdout);
  had_err = test(err);
  if (had_err) {
    gt_xputs("error");
    *had_errp = had_err;
    fprintf(stderr, "first error: %s\n", gt_error_get(err));
    gt_error_unset(err);
    gt_xfflush(stderr);
  }
  else
    gt_xputs("ok");
  gt_xfflush(stdout);
  return 0;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
movq %rcx, %rbx
movq %rdx, %r14
movq %rsi, %r15
movq %rdi, %r12
testq %rcx, %rcx
je 0xb2b41
movq %rbx, %rdi
callq 0x89eb7
testb %al, %al
jne 0xb2c1a
testq %r12, %r12
je 0xb2bf0
testq %r15, %r15
je 0xb2bf0
testq %r14, %r14
je 0xb2bf0
leaq 0x2b39f9(%rip), %rdi    # 0x36655c
movq %r12, %rsi
xorl %eax, %eax
callq 0x17070
movq 0x38533c(%rip), %r12    # 0x437eb0
movq (%r12), %rdi
callq 0xb2e24
movq %rbx, %rdi
callq *%r15
testl %eax, %eax
jne 0xb2ba7
leaq 0x25a00c(%rip), %rdi    # 0x30cb9a
callq 0xb30e8
movq (%r12), %rdi
callq 0xb2e24
xorl %eax, %eax
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq
movl %eax, %ebp
leaq 0x2c7c0a(%rip), %rdi    # 0x37a7ba
callq 0xb30e8
movl %ebp, (%r14)
movq 0x3853a9(%rip), %r15    # 0x437f68
movq (%r15), %r14
movq %rbx, %rdi
callq 0x89f41
leaq 0x26150e(%rip), %rsi    # 0x3140df
movq %r14, %rdi
movq %rax, %rdx
xorl %eax, %eax
callq 0x17a50
movq %rbx, %rdi
callq 0x89efa
movq (%r15), %rdi
callq 0xb2e24
jmp 0xb2b93
movq 0x385371(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x232412(%rip), %rsi    # 0x2e5013
leaq 0x2614be(%rip), %rdx    # 0x3140c6
leaq 0x26148e(%rip), %rcx    # 0x31409d
leaq 0x261498(%rip), %r8     # 0x3140ae
pushq $0x1b
jmp 0xb2c42
movq 0x385347(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x2323e8(%rip), %rsi    # 0x2e5013
leaq 0x23258d(%rip), %rdx    # 0x2e51bf
leaq 0x261464(%rip), %rcx    # 0x31409d
leaq 0x26146e(%rip), %r8     # 0x3140ae
pushq $0x1a
popq %r9
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/extended/aligned_segments_pile.c
// Function: gt_aligned_segments_pile_new
GtAlignedSegmentsPile *gt_aligned_segments_pile_new(GtSamfileIterator *sfi,
    GtSamfileEncseqMapping *sem)
{
  GtAlignedSegmentsPile *asp;
  gt_assert(sfi != NULL);
  gt_assert(sem != NULL);
  asp = gt_malloc(sizeof (GtAlignedSegmentsPile));
  asp->sfi = sfi;
  asp->sem = sem;
  asp->set = gt_dlist_new(gt_aligned_segments_pile_compare_as);
  asp->all_consumed = false;
  asp->next_as = NULL;
  asp->process_complete = NULL;
  asp->process_complete_data = NULL;
  asp->process_unmapped = NULL;
  asp->process_unmapped_data = NULL;
  asp->process_skipped = NULL;
  asp->process_skipped_data = NULL;
  asp->position = GT_UNDEF_UWORD;
  asp->enable_edit_tracking = false;
  asp->delete_processed_segments = true;
  return asp;
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
testq %rdi, %rdi
je 0xb47ae
movq %rsi, %rbx
testq %rsi, %rsi
je 0xb47d8
movq %rdi, %r14
leaq 0x260540(%rip), %rsi    # 0x314c98
pushq $0x68
popq %rdi
pushq $0x38
popq %rdx
callq 0x93160
movq %rax, %r15
movq %r14, (%rax)
movq %rbx, 0x8(%rax)
leaq -0x68(%rip), %rdi       # 0xb470c
callq 0x6e154
movq %rax, 0x10(%r15)
movb $0x0, 0x20(%r15)
andq $0x0, 0x18(%r15)
xorps %xmm0, %xmm0
movups %xmm0, 0x28(%r15)
movups %xmm0, 0x38(%r15)
movups %xmm0, 0x48(%r15)
orq $-0x1, 0x58(%r15)
movw $0x100, 0x60(%r15)      # imm = 0x100
movq %r15, %rax
popq %rbx
popq %r14
popq %r15
retq
movq 0x3837b3(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x230854(%rip), %rsi    # 0x2e5013
leaq 0x2604a9(%rip), %rdx    # 0x314c6f
leaq 0x2604ae(%rip), %rcx    # 0x314c7b
leaq 0x2604c4(%rip), %r8     # 0x314c98
pushq $0x36
jmp 0xb4800
movq 0x383789(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x23082a(%rip), %rsi    # 0x2e5013
leaq 0x2604cd(%rip), %rdx    # 0x314cbd
leaq 0x260484(%rip), %rcx    # 0x314c7b
leaq 0x26049a(%rip), %r8     # 0x314c98
pushq $0x37
popq %r9
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/extended/aligned_segments_pile.c
// Function: gt_aligned_segments_pile_disable_segment_deletion
void gt_aligned_segments_pile_disable_segment_deletion(
    GtAlignedSegmentsPile *asp)
{
  gt_assert(asp != NULL);
  gt_assert(asp->process_skipped != NULL);
  gt_assert(asp->process_complete != NULL);
  gt_assert(asp->process_unmapped != NULL);
  asp->delete_processed_segments = false;
}

// Assembly:
pushq %rax
testq %rdi, %rdi
je 0xb4902
cmpq $0x0, 0x48(%rdi)
je 0xb4933
cmpq $0x0, 0x28(%rdi)
je 0xb4961
cmpq $0x0, 0x38(%rdi)
je 0xb498f
movb $0x0, 0x61(%rdi)
popq %rax
retq
movq 0x38365f(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x230700(%rip), %rsi    # 0x2e5013
leaq 0x2603af(%rip), %rdx    # 0x314cc9
leaq 0x26044c(%rip), %rcx    # 0x314d6d
leaq 0x260370(%rip), %r8     # 0x314c98
movl $0xae, %r9d
jmp 0xb49bb
movq 0x38362e(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x2306cf(%rip), %rsi    # 0x2e5013
leaq 0x260454(%rip), %rdx    # 0x314d9f
leaq 0x26041b(%rip), %rcx    # 0x314d6d
leaq 0x26033f(%rip), %r8     # 0x314c98
movl $0xaf, %r9d
jmp 0xb49bb
movq 0x383600(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x2306a1(%rip), %rsi    # 0x2e5013
leaq 0x260443(%rip), %rdx    # 0x314dbc
leaq 0x2603ed(%rip), %rcx    # 0x314d6d
leaq 0x260311(%rip), %r8     # 0x314c98
movl $0xb0, %r9d
jmp 0xb49bb
movq 0x3835d2(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x230673(%rip), %rsi    # 0x2e5013
leaq 0x260433(%rip), %rdx    # 0x314dda
leaq 0x2603bf(%rip), %rcx    # 0x314d6d
leaq 0x2602e3(%rip), %r8     # 0x314c98
movl $0xb1, %r9d
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/extended/aligned_segments_pile.c
// Function: gt_aligned_segments_pile_move_over_position
void gt_aligned_segments_pile_move_over_position(
    GtAlignedSegmentsPile *asp, GtUword position)
{
  int retvalue;
  if (asp->position != GT_UNDEF_UWORD)
  {
    gt_assert(position > asp->position);
    gt_aligned_segments_pile_delete_finishing_before(asp, position);
  }
  while (true)
  {
    if (asp->next_as == NULL && !asp->all_consumed)
    {
      retvalue = gt_aligned_segments_pile_fetch_sa(asp);
      if (retvalue == -1)
      {
        asp->all_consumed = true;
        gt_assert(asp->next_as == NULL);
      }
    }
    if (asp->next_as != NULL)
    {
      if (gt_aligned_segment_refregion_endpos(asp->next_as) < position)
      {
        if (asp->process_skipped != NULL)
        {
          asp->process_skipped(asp->next_as, asp->process_unmapped_data);
        }
        if (asp->delete_processed_segments)
          gt_aligned_segment_delete(asp->next_as);
        asp->next_as = NULL;
      }
      else
      {
        if (gt_aligned_segment_refregion_startpos(asp->next_as) <= position)
        {
          gt_dlist_add(asp->set, asp->next_as);
          asp->next_as = NULL;
        }
        else
        {
          break;
        }
      }
    }
    else
    {
      break;
    }
  }
  asp->position = position;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rsi, %rbx
movq %rdi, %r14
movq 0x58(%rdi), %rax
cmpq $-0x1, %rax
je 0xb4a79
cmpq %rbx, %rax
jae 0xb4b08
movq %r14, %rdi
movq %rbx, %rsi
callq 0xb4b6e
movq 0x18(%r14), %rdi
testq %rdi, %rdi
jne 0xb4a9f
cmpb $0x0, 0x20(%r14)
jne 0xb4afc
movq %r14, %rdi
callq 0xb4c0a
movq 0x18(%r14), %rdi
cmpl $-0x1, %eax
je 0xb4af2
testq %rdi, %rdi
je 0xb4afc
callq 0x29647c
cmpq %rbx, %rax
jae 0xb4ace
movq 0x48(%r14), %rax
testq %rax, %rax
je 0xb4abc
movq 0x18(%r14), %rdi
movq 0x40(%r14), %rsi
callq *%rax
cmpb $0x1, 0x61(%r14)
jne 0xb4ae9
movq 0x18(%r14), %rdi
callq 0x296acb
jmp 0xb4ae9
movq 0x18(%r14), %rdi
callq 0x296439
cmpq %rbx, %rax
ja 0xb4afc
movq 0x10(%r14), %rdi
movq 0x18(%r14), %rsi
callq 0x6e34e
andq $0x0, 0x18(%r14)
xorl %edi, %edi
jmp 0xb4a7d
movb $0x1, 0x20(%r14)
testq %rdi, %rdi
jne 0xb4b36
movq %rbx, 0x58(%r14)
addq $0x8, %rsp
popq %rbx
popq %r14
retq
movq 0x383459(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x2304fa(%rip), %rsi    # 0x2e5013
leaq 0x260324(%rip), %rdx    # 0x314e44
leaq 0x260336(%rip), %rcx    # 0x314e5d
leaq 0x26016a(%rip), %r8     # 0x314c98
movl $0xc7, %r9d
jmp 0xb4b62
movq 0x38342b(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x2304cc(%rip), %rsi    # 0x2e5013
leaq 0x26033b(%rip), %rdx    # 0x314e89
leaq 0x260308(%rip), %rcx    # 0x314e5d
leaq 0x26013c(%rip), %r8     # 0x314c98
movl $0xd2, %r9d
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/extended/aligned_segments_pile.c
// Function: gt_aligned_segments_pile_delete_finishing_before
static void gt_aligned_segments_pile_delete_finishing_before(
    GtAlignedSegmentsPile *asp, GtUword position)
{
  GtDlistelem *dlistelem, *dlistelem_to_remove = NULL;
  for (dlistelem = gt_dlist_first(asp->set); dlistelem != NULL;
       dlistelem = gt_dlistelem_next(dlistelem))
  {
    GtAlignedSegment *as;
    if (dlistelem_to_remove != NULL)
    {
      gt_dlist_remove(asp->set, dlistelem_to_remove);
      dlistelem_to_remove = NULL;
    }
    as = gt_dlistelem_get_data(dlistelem);
    if (gt_aligned_segment_refregion_endpos(as) < position)
    {
      if (asp->process_complete != NULL)
      {
        asp->process_complete(as, asp->process_complete_data);
      }
      if (asp->delete_processed_segments)
        gt_aligned_segment_delete(as);
      /* delay elem removal to avoid disrupting list traversal */
      dlistelem_to_remove = dlistelem;
    }
    else
    {
      break;
    }
  }
  if (dlistelem_to_remove != NULL)
  {
    gt_dlist_remove(asp->set, dlistelem_to_remove);
    dlistelem_to_remove = NULL;
  }
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
movq %rsi, %r14
movq %rdi, %rbx
movq 0x10(%rdi), %rdi
callq 0x6e1b4
movq %rax, %r15
xorl %esi, %esi
testq %r15, %r15
je 0xb4be5
testq %rsi, %rsi
je 0xb4b9d
movq 0x10(%rbx), %rdi
callq 0x6e631
movq %r15, %rdi
callq 0x6e2bb
movq %rax, %r12
movq %rax, %rdi
callq 0x29647c
cmpq %r14, %rax
jae 0xb4bfe
movq 0x28(%rbx), %rax
testq %rax, %rax
je 0xb4bc7
movq 0x30(%rbx), %rsi
movq %r12, %rdi
callq *%rax
cmpb $0x1, 0x61(%rbx)
jne 0xb4bd5
movq %r12, %rdi
callq 0x296acb
movq %r15, %rdi
callq 0x6e2fe
movq %r15, %rsi
movq %rax, %r15
jmp 0xb4b8a
testq %rsi, %rsi
je 0xb4bfe
movq 0x10(%rbx), %rdi
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
jmp 0x6e631
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/extended/aligned_segments_pile.c
// Function: gt_aligned_segments_pile_fetch_sa
static int gt_aligned_segments_pile_fetch_sa(GtAlignedSegmentsPile *asp)
{
  int retvalue;
  GtSamAlignment *sa;
  gt_assert(asp != NULL);
  gt_assert(asp->next_as == NULL);
  while (true)
  {
    retvalue = gt_samfile_iterator_next(asp->sfi, &sa);
    if (retvalue == -1 || !gt_sam_alignment_is_unmapped(sa))
      break;
    if (!gt_sam_alignment_is_secondary(sa))
    {
      if (asp->process_unmapped != NULL)
      {
        GtAlignedSegment *as = gt_aligned_segment_new_from_sa(sa, asp->sem);
        if (asp->enable_edit_tracking)
          gt_aligned_segment_enable_edit_tracking(as);
        asp->process_unmapped(as, asp->process_unmapped_data);
        if (asp->delete_processed_segments)
          gt_aligned_segment_delete(as);
      }
    }
  }
  if (retvalue != -1)
  {
    asp->next_as = gt_aligned_segment_new_from_sa(sa, asp->sem);
    if (asp->enable_edit_tracking)
      gt_aligned_segment_enable_edit_tracking(asp->next_as);
  }
  return retvalue;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0xb4cbe
movq %rdi, %rbx
cmpq $0x0, 0x18(%rdi)
jne 0xb4ce8
movq %rsp, %r14
movq (%rbx), %rdi
movq %r14, %rsi
callq 0x113c62
movl %eax, %ebp
cmpl $-0x1, %eax
je 0xb4cb1
movq (%rsp), %rdi
callq 0x1133d0
movq (%rsp), %rdi
testb %al, %al
je 0xb4c96
callq 0x11358a
testb %al, %al
jne 0xb4c2b
cmpq $0x0, 0x38(%rbx)
je 0xb4c2b
movq (%rsp), %rdi
movq 0x8(%rbx), %rsi
callq 0x295c38
movq %rax, %r15
cmpb $0x1, 0x60(%rbx)
jne 0xb4c7c
movq %r15, %rdi
callq 0x296203
movq 0x40(%rbx), %rsi
movq %r15, %rdi
callq *0x38(%rbx)
cmpb $0x1, 0x61(%rbx)
jne 0xb4c2b
movq %r15, %rdi
callq 0x296acb
jmp 0xb4c2b
movq 0x8(%rbx), %rsi
callq 0x295c38
movq %rax, 0x18(%rbx)
cmpb $0x1, 0x60(%rbx)
jne 0xb4cb1
movq %rax, %rdi
callq 0x296203
movl %ebp, %eax
addq $0x8, %rsp
popq %rbx
popq %r14
popq %r15
popq %rbp
retq
movq 0x3832a3(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x230344(%rip), %rsi    # 0x2e5013
leaq 0x25fff3(%rip), %rdx    # 0x314cc9
leaq 0x2601fd(%rip), %rcx    # 0x314eda
leaq 0x25ffb4(%rip), %r8     # 0x314c98
pushq $0x69
jmp 0xb4d10
movq 0x383279(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x23031a(%rip), %rsi    # 0x2e5013
leaq 0x260189(%rip), %rdx    # 0x314e89
leaq 0x2601d3(%rip), %rcx    # 0x314eda
leaq 0x25ff8a(%rip), %r8     # 0x314c98
pushq $0x6a
popq %r9
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/extended/aligned_segments_pile.c
// Function: gt_aligned_segments_pile_flush
void gt_aligned_segments_pile_flush(GtAlignedSegmentsPile *asp,
    bool skip_remaining)
{
  gt_assert(asp != NULL);
  gt_aligned_segments_pile_delete_finishing_before(asp, ULONG_MAX);
  if (asp->next_as != NULL)
  {
    if (skip_remaining && asp->process_skipped != NULL)
    {
      asp->process_skipped(asp->next_as, asp->process_skipped_data);
    }
    if (asp->delete_processed_segments)
      gt_aligned_segment_delete(asp->next_as);
    asp->next_as = NULL;
  }
  if (skip_remaining && asp->process_skipped != NULL)
  {
    int retvalue = 0;
    while (retvalue != -1)
    {
      retvalue = gt_aligned_segments_pile_fetch_sa(asp);
      if (asp->next_as != NULL)
      {
        asp->process_skipped(asp->next_as, asp->process_skipped_data);
      }
      if (asp->delete_processed_segments)
        gt_aligned_segment_delete(asp->next_as);
      asp->next_as = NULL;
    }
  }
  gt_assert(asp->next_as == NULL);
}

// Assembly:
pushq %rbp
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0xb4df5
movl %esi, %ebp
movq %rdi, %rbx
pushq $-0x1
popq %rsi
callq 0xb4b6e
movq 0x18(%rbx), %rdi
testq %rdi, %rdi
je 0xb4dab
testb %bpl, %bpl
je 0xb4d97
movq 0x48(%rbx), %rax
testq %rax, %rax
je 0xb4d97
movq 0x50(%rbx), %rsi
callq *%rax
cmpb $0x1, 0x61(%rbx)
jne 0xb4da6
movq 0x18(%rbx), %rdi
callq 0x296acb
andq $0x0, 0x18(%rbx)
testb %bpl, %bpl
je 0xb4dee
cmpq $0x0, 0x48(%rbx)
je 0xb4dee
xorl %ebp, %ebp
cmpl $-0x1, %ebp
je 0xb4dee
movq %rbx, %rdi
callq 0xb4c0a
movl %eax, %ebp
movq 0x18(%rbx), %rdi
testq %rdi, %rdi
je 0xb4dd8
movq 0x50(%rbx), %rsi
callq *0x48(%rbx)
cmpb $0x1, 0x61(%rbx)
jne 0xb4de7
movq 0x18(%rbx), %rdi
callq 0x296acb
andq $0x0, 0x18(%rbx)
jmp 0xb4db9
addq $0x8, %rsp
popq %rbx
popq %rbp
retq
movq 0x38316c(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x23020d(%rip), %rsi    # 0x2e5013
leaq 0x25febc(%rip), %rdx    # 0x314cc9
leaq 0x2600a7(%rip), %rcx    # 0x314ebb
leaq 0x25fe7d(%rip), %r8     # 0x314c98
movl $0xff, %r9d
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/extended/aligned_segments_pile.c
// Function: gt_aligned_segments_pile_delete
void gt_aligned_segments_pile_delete(GtAlignedSegmentsPile *asp)
{
  if (asp != NULL)
  {
    gt_aligned_segments_pile_flush(asp, true);
    gt_dlist_delete(asp->set);
    gt_free(asp);
  }
}

// Assembly:
testq %rdi, %rdi
je 0xb4e5c
pushq %rbx
movq %rdi, %rbx
pushq $0x1
popq %rsi
callq 0xb4d61
movq 0x10(%rbx), %rdi
callq 0x6e7d8
leaq 0x25fe4a(%rip), %rsi    # 0x314c98
movq %rbx, %rdi
movl $0x123, %edx            # imm = 0x123
popq %rbx
jmp 0x936f9
retq
nopl (%rax)
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/extended/alignment.c
// Function: gt_alignment_new
GtAlignment* gt_alignment_new(void)
{
  GtAlignment *alignment;
  alignment = gt_calloc((size_t) 1, sizeof (GtAlignment));
  alignment->aligned_range_u.start = 0;
  alignment->aligned_range_u.end = 0;
  alignment->aligned_range_v.start = 0;
  alignment->aligned_range_v.end = 0;
  alignment->eops = gt_multieoplist_new();
  alignment->u = alignment->v = NULL;
  alignment->alilen = alignment->ulen = alignment->vlen = 0;
  return alignment;
}

// Assembly:
pushq %rbx
leaq 0x2600a8(%rip), %rdx    # 0x314f10
pushq $0x1
popq %rdi
pushq $0x50
popq %rsi
pushq $0x38
popq %rcx
callq 0x9334a
movq %rax, %rbx
xorps %xmm0, %xmm0
movups %xmm0, (%rax)
movups %xmm0, 0x10(%rax)
callq 0x101648
movq %rax, 0x30(%rbx)
xorps %xmm0, %xmm0
movups %xmm0, 0x20(%rbx)
movups %xmm0, 0x38(%rbx)
andq $0x0, 0x48(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/extended/alignment.c
// Function: gt_alignment_new_with_seqs
GtAlignment* gt_alignment_new_with_seqs(const GtUchar *u, GtUword ulen,
                                        const GtUchar *v, GtUword vlen)
{
  GtAlignment *alignment;

  gt_assert(u != NULL && v != NULL);
  alignment = gt_alignment_new();
  gt_alignment_set_seqs(alignment, u, ulen, v, vlen);
  return alignment;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
testq %rdi, %rdi
je 0xb4ee9
movq %rdx, %r14
testq %rdx, %rdx
je 0xb4ee9
movq %rcx, %rbx
movq %rsi, %r15
movq %rdi, %r12
callq 0xb4e60
movq %rax, %r13
movq %rax, %rdi
movq %r12, %rsi
movq %r15, %rdx
movq %r14, %rcx
movq %rbx, %r8
callq 0xb4f1f
movq %r13, %rax
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
retq
movq 0x383078(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x230119(%rip), %rsi    # 0x2e5013
leaq 0x260058(%rip), %rdx    # 0x314f59
leaq 0x260021(%rip), %rcx    # 0x314f29
leaq 0x260001(%rip), %r8     # 0x314f10
pushq $0x48
popq %r9
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/extended/alignment.c
// Function: gt_alignment_set_seqs
void gt_alignment_set_seqs(GtAlignment *alignment, const GtUchar *u,
                           GtUword ulen, const GtUchar *v,
                           GtUword vlen)
{
  gt_assert(alignment != NULL && u != NULL && v != NULL);
  alignment->u = u;
  alignment->v = v;
  alignment->ulen = ulen;
  alignment->vlen = vlen;
  alignment->aligned_range_u.start = alignment->aligned_range_v.start = 0;
  alignment->aligned_range_u.end = ulen - 1;
  alignment->aligned_range_v.end = vlen - 1;
}

// Assembly:
testq %rdi, %rdi
je 0xb4f56
testq %rsi, %rsi
je 0xb4f56
testq %rcx, %rcx
je 0xb4f56
movq %rsi, 0x20(%rdi)
movq %rcx, 0x28(%rdi)
movq %rdx, 0x38(%rdi)
movq %r8, 0x40(%rdi)
andq $0x0, 0x10(%rdi)
andq $0x0, (%rdi)
decq %rdx
movq %rdx, 0x8(%rdi)
decq %r8
movq %r8, 0x18(%rdi)
retq
pushq %rax
movq 0x38300a(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x2300ab(%rip), %rsi    # 0x2e5013
leaq 0x25ffd5(%rip), %rdx    # 0x314f44
leaq 0x25fffa(%rip), %rcx    # 0x314f70
leaq 0x25ff93(%rip), %r8     # 0x314f10
pushq $0x52
popq %r9
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/extended/alignment.c
// Function: gt_alignment_set_multieop_list
void gt_alignment_set_multieop_list(GtAlignment *alignment,
                                    GtMultieoplist *eoplist)
{
  gt_assert(alignment != NULL && eoplist != NULL);
  gt_multieoplist_delete(alignment->eops);
  alignment->eops = gt_multieoplist_ref(eoplist);
  alignment->alilen = gt_multieoplist_get_num_entries(eoplist);
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0xb4fca
movq %rsi, %r14
testq %rsi, %rsi
je 0xb4fca
movq %rdi, %rbx
movq 0x30(%rdi), %rdi
callq 0x101766
movq %r14, %rdi
callq 0x10175f
movq %rax, 0x30(%rbx)
movq %r14, %rdi
callq 0x101b46
movq %rax, 0x48(%rbx)
addq $0x8, %rsp
popq %rbx
popq %r14
retq
movq 0x382f97(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x230038(%rip), %rsi    # 0x2e5013
leaq 0x25ffa4(%rip), %rdx    # 0x314f86
leaq 0x25ffc2(%rip), %rcx    # 0x314fab
leaq 0x25ff20(%rip), %r8     # 0x314f10
pushq $0x5f
popq %r9
xorl %eax, %eax
callq 0x17a50
callq 0x17390
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/extended/alignment.c
// Function: gt_alignment_is_valid
static bool gt_alignment_is_valid(const GtAlignment *alignment)
{
  GtUword len;
  /* check ulen */
  len = gt_multieoplist_get_repdel_length(alignment->eops);
  if (len != alignment->ulen) {
    printf("ulen: " GT_WU ", repdel: " GT_WU "\n", alignment->ulen, len);
    return false;
  }
  /* check vlen */
  len = gt_multieoplist_get_repins_length(alignment->eops);
  if (len != alignment->vlen) {
    printf("vlen: " GT_WU ", repins: " GT_WU "\n", alignment->vlen, len);
    return false;
  }
  return true;
}

// Assembly:
pushq %rbx
movq %rdi, %rbx
movq 0x30(%rdi), %rdi
callq 0x1019fc
movq 0x38(%rbx), %rsi
cmpq %rsi, %rax
jne 0xb55a7
movq 0x30(%rbx), %rdi
callq 0x101a70
movq 0x40(%rbx), %rsi
movb $0x1, %bl
cmpq %rsi, %rax
je 0xb55ba
leaq 0x25fdf2(%rip), %rdi    # 0x315397
jmp 0xb55ae
leaq 0x25fdd1(%rip), %rdi    # 0x31537f
xorl %ebx, %ebx
movq %rax, %rdx
xorl %eax, %eax
callq 0x17070
movl %ebx, %eax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/extended/alignment.c
// Function: gt_alignment_show_advance
static unsigned int gt_alignment_show_advance(unsigned int pos,
                                              unsigned int width,
                                              const GtUchar *topbuf,
                                              FILE *fp)
{
  gt_assert(width > 0);
  if (pos < width - 1)
  {
    return pos + 1;
  }
  gt_assert(pos == width - 1);
  fwrite(topbuf,sizeof *topbuf,3 * (width+1),fp);
  return 0;
}

// Assembly:
pushq %rax
testl %esi, %esi
je 0xb5fe6
leal -0x1(%rsi), %eax
cmpl %edi, %eax
jbe 0xb5fca
incl %edi
jmp 0xb5fe2
jne 0xb6014
leal (%rsi,%rsi,2), %eax
addl $0x3, %eax
pushq $0x1
popq %rsi
movq %rdx, %rdi
movq %rax, %rdx
callq 0x17f00
xorl %edi, %edi
movl %edi, %eax
popq %rcx
retq
movq 0x381f7b(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x22f01c(%rip), %rsi    # 0x2e5013
leaq 0x2cd61c(%rip), %rdx    # 0x38361a
leaq 0x25f3fb(%rip), %rcx    # 0x315400
leaq 0x25ef04(%rip), %r8     # 0x314f10
movl $0x206, %r9d            # imm = 0x206
jmp 0xb6040
movq 0x381f4d(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x22efee(%rip), %rsi    # 0x2e5013
leaq 0x25f3ee(%rip), %rdx    # 0x31541a
leaq 0x25f3cd(%rip), %rcx    # 0x315400
leaq 0x25eed6(%rip), %r8     # 0x314f10
movl $0x20b, %r9d            # imm = 0x20B
xorl %eax, %eax
callq 0x17a50
callq 0x17390