// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/jkOwnLib/genoFind.c
// Function: gfFindClumpsWithQmask
struct gfClump *gfFindClumpsWithQmask(struct genoFind *gf, bioSeq *seq, 
	Bits *qMaskBits, int qMaskOffset,
	struct lm *lm, int *retHitCount)
/* Find clumps associated with one sequence soft-masking seq according to qMaskBits */
{
    struct gfClump *clumpList = NULL;
    struct gfHit *hitList;
    int minMatch = gf->minMatch;

    int cmpQuerySize;

    #ifdef OLD	/* stepSize makes this obsolete. */
    if (seq->size < gf->tileSize * (gf->minMatch+1))
         minMatch = 1;
    #endif /* OLD */

    hitList =  gfFindHitsWithQmask(gf, seq, qMaskBits, qMaskOffset, lm,
                                   retHitCount, NULL, 0, 0);
    cmpQuerySize = seq->size;
    clumpList = clumpHits(gf, hitList, minMatch);
    return clumpList;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x68, %rsp
movq %rdi, %rbx
movl 0x4(%rdi), %eax
movl %eax, 0x14(%rsp)
subq $0x8, %rsp
pushq $0x0
pushq $0x0
pushq $0x0
callq 0xc091
addq $0x20, %rsp
movq %rax, %r14
andq $0x0, 0x18(%rsp)
movl 0x8(%rbx), %ebp
movl 0xc(%rbx), %r15d
movzwl 0x32(%rbx), %eax
movq %rbx, 0x30(%rsp)
movb 0x28(%rbx), %bl
movq %rax, %r12
leaq 0x8(,%rax,8), %rdi
callq 0x28a1f
movq %rax, 0x38(%rsp)
testq %r14, %r14
je 0xbd9f
movq (%r14), %rcx
movzwl 0xe(%r14), %edx
movq (%rax,%rdx,8), %rsi
movq %rsi, (%r14)
movq %r14, (%rax,%rdx,8)
movq %rcx, %r14
jmp 0xbd82
movq %r15, 0x48(%rsp)
testb %bl, %bl
movl $0xfed4, %eax           # imm = 0xFED4
movl $0xff9c, %ecx           # imm = 0xFF9C
cmovel %eax, %ecx
movl %ecx, 0x2c(%rsp)
movl %r12d, %eax
movq %rax, 0x60(%rsp)
incl %r12d
movq %r12, 0x50(%rsp)
xorl %r13d, %r13d
cmpq 0x50(%rsp), %r13
je 0xbe9d
movq 0x38(%rsp), %rax
leaq (%rax,%r13,8), %rbx
movq %rbx, %rdi
callq 0xbae1
movq %rbx, 0x58(%rsp)
movq (%rbx), %r12
leaq 0x1(%r13), %rbx
testq %r12, %r12
je 0xbe84
xorl %r14d, %r14d
xorl %r15d, %r15d
xorl %eax, %eax
testq %r12, %r12
je 0xbe37
movq (%r12), %rcx
testq %r14, %r14
je 0xbe1e
movl 0x10(%r12), %edx
subl 0x10(%r14), %edx
cmpl %ebp, %edx
ja 0xbe37
movl 0xc(%r12), %edx
cmpl %eax, %edx
cmoval %edx, %eax
movq %r14, (%r12)
incl %r15d
movq %r12, %r14
movq %rcx, %r12
jmp 0xbe03
cmpq 0x60(%rsp), %r13
jae 0xbe5b
cmpl 0x2c(%rsp), %eax
jbe 0xbe5b
movq 0x38(%rsp), %r15
movq (%r15,%rbx,8), %rsi
movq %r14, %rdi
callq 0x1c549
movq %rax, (%r15,%rbx,8)
jmp 0xbdf2
cmpl 0x14(%rsp), %r15d
jl 0xbdf2
pushq $0x38
popq %rdi
callq 0x28bb0
movq 0x18(%rsp), %rcx
movq %rcx, (%rax)
movq %rax, 0x18(%rsp)
movl %r15d, 0x20(%rax)
movq %r14, 0x28(%rax)
jmp 0xbdf2
movq 0x58(%rsp), %rax
andq $0x0, (%rax)
addl $0x10000, 0x2c(%rsp)    # imm = 0x10000
movq %rbx, %r13
jmp 0xbdca
movq 0x18(%rsp), %r14
leaq 0x20(%rsp), %rax
andq $0x0, (%rax)
movq 0x30(%rsp), %rax
movl 0xc(%rax), %ebp
cmpb $0x0, 0x28(%rax)
movl $0x12c, %eax            # imm = 0x12C
pushq $0x64
popq %r15
cmovel %eax, %r15d
movq %r14, 0x8(%rsp)
testq %r14, %r14
je 0xbfe9
andq $0x0, (%rsp)
movq 0x28(%r14), %rax
movq %rax, 0x40(%rsp)
andl $0x0, 0x20(%r14)
andq $0x0, 0x28(%r14)
movq (%r14), %r14
leaq 0x40(%rsp), %rdi
leaq 0x166d(%rip), %rsi      # 0xd566
callq 0x1c5ab
movq 0x40(%rsp), %rbx
movl 0xc(%rbx), %ecx
xorl %r13d, %r13d
testq %rbx, %rbx
je 0xbf9a
movq (%rbx), %r12
movl 0xc(%rbx), %eax
addl %r15d, %ecx
cmpl %ecx, %eax
jbe 0xbf82
cmpl 0x14(%rsp), %r13d
jge 0xbf36
andq $0x0, (%rsp)
movq 0x8(%rsp), %rcx
andl $0x0, 0x20(%rcx)
jmp 0xbf7f
movq %rsp, %rdi
callq 0x1c567
movq (%rsp), %rax
movq 0x8(%rsp), %rdi
movq %rax, 0x28(%rdi)
andq $0x0, (%rsp)
movl %r13d, 0x20(%rdi)
movl %ebp, %esi
callq 0xd584
movq 0x8(%rsp), %rdx
movq 0x30(%rsp), %rdi
leaq 0x20(%rsp), %rsi
callq 0xd5ec
pushq $0x38
popq %rdi
callq 0x28bb0
movq %rax, 0x8(%rsp)
movl 0xc(%rbx), %eax
xorl %r13d, %r13d
movq (%rsp), %rcx
movq %rcx, (%rbx)
movq %rbx, (%rsp)
incl %r13d
movl %eax, %ecx
movq %r12, %rbx
jmp 0xbf09
movq %rsp, %rdi
callq 0x1c567
movq (%rsp), %rax
movq 0x8(%rsp), %rdi
movq %rax, 0x28(%rdi)
cmpl 0x14(%rsp), %r13d
jge 0xbfc5
leaq 0x8(%rsp), %rdi
callq 0xba53
jmp 0xbec4
movl %r13d, 0x20(%rdi)
movl %ebp, %esi
callq 0xd584
movq 0x8(%rsp), %rdx
movq 0x30(%rsp), %rdi
leaq 0x20(%rsp), %rsi
callq 0xd5ec
jmp 0xbec4
leaq 0x20(%rsp), %r15
movq (%r15), %rbx
movq %rbx, 0x18(%rsp)
leaq 0x1721(%rip), %r14      # 0xd71e
movq 0x48(%rsp), %r12
testq %rbx, %rbx
je 0xc061
movq 0x28(%rbx), %rax
movq %rax, 0x20(%rsp)
testq %rax, %rax
je 0xc05c
movq %r15, %rdi
movq %r14, %rsi
callq 0x1c5ab
movq 0x20(%rsp), %rcx
movl 0x8(%rcx), %esi
leal (%rsi,%r12), %edx
xorl %eax, %eax
testq %rcx, %rcx
je 0xc055
movl 0x8(%rcx), %edi
cmpl %edx, %edi
jbe 0xc046
subl %esi, %eax
addl %edx, %eax
leal (%rdi,%r12), %edx
movl %edi, %esi
jmp 0xc050
addl %r12d, %edi
cmpl %edx, %edi
cmovbel %edx, %edi
movl %edi, %edx
movq (%rcx), %rcx
jmp 0xc02e
subl %esi, %eax
addl %edx, %eax
movl %eax, 0x30(%rbx)
movq (%rbx), %rbx
jmp 0xc002
leaq 0x14f1(%rip), %rsi      # 0xd559
leaq 0x18(%rsp), %rbx
movq %rbx, %rdi
callq 0x1c5ab
leaq 0x38(%rsp), %rdi
callq 0x28c3d
movq (%rbx), %rax
addq $0x68, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq