// File: /workspace/github_c_makefile_star2_O3/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, %r15
movl 0x4(%rdi), %eax
movl %eax, 0x14(%rsp)
subq $0x8, %rsp
xorl %ebx, %ebx
pushq %rbx
pushq %rbx
pushq %rbx
callq 0xe287
addq $0x20, %rsp
movq %rax, %r14
movq %rbx, 0x20(%rsp)
movl 0x8(%r15), %eax
movl %eax, 0x3c(%rsp)
movl 0xc(%r15), %eax
movq %rax, 0x48(%rsp)
movzwl 0x32(%r15), %ecx
movq %r15, 0x28(%rsp)
cmpb $0x0, 0x28(%r15)
movl $0xfed4, %eax           # imm = 0xFED4
movl $0xff9c, %ebp           # imm = 0xFF9C
cmovel %eax, %ebp
movq %rcx, %rbx
leaq 0x8(,%rcx,8), %rdi
callq 0x2de63
movq %rax, 0x30(%rsp)
testq %r14, %r14
je 0xdf6f
movq (%r14), %rcx
movzwl 0xe(%r14), %edx
movq (%rax,%rdx,8), %rsi
movq %rsi, (%r14)
movq %r14, (%rax,%rdx,8)
movq %rcx, %r14
testq %rcx, %rcx
jne 0xdf54
movq %rbx, %rax
movl %eax, %ebx
incl %eax
movq %rax, 0x50(%rsp)
xorl %r14d, %r14d
movq 0x30(%rsp), %rax
leaq (%rax,%r14,8), %r15
movq %r15, %rdi
callq 0xdc74
movq (%r15), %r13
testq %r13, %r13
je 0xe059
movq %r15, 0x60(%rsp)
leaq 0x1(%r14), %rax
movq %rax, 0x58(%rsp)
xorl %eax, %eax
xorl %r12d, %r12d
xorl %r15d, %r15d
movq %r13, %rcx
movq (%r13), %r13
testq %r15, %r15
je 0xdfcf
movl 0x10(%rcx), %edx
subl 0x10(%r15), %edx
cmpl 0x3c(%rsp), %edx
jbe 0xdfcf
movq %rcx, %r13
jmp 0xdfeb
movl 0xc(%rcx), %edx
cmpl %eax, %edx
cmoval %edx, %eax
movq %r15, (%rcx)
incl %r12d
movq %rcx, %r15
testq %r13, %r13
jne 0xdfb1
movq %rcx, %r15
xorl %r13d, %r13d
cmpq %rbx, %r14
jae 0xe00d
cmpl %ebp, %eax
jbe 0xe00d
movq 0x30(%rsp), %r12
movq 0x8(%r12,%r14,8), %rsi
movq %r15, %rdi
callq 0x20155
movq %rax, 0x8(%r12,%r14,8)
jmp 0xe033
cmpl 0x14(%rsp), %r12d
jl 0xe033
movl $0x38, %edi
callq 0x2dff4
movq 0x20(%rsp), %rcx
movq %rcx, (%rax)
movq %rax, 0x20(%rsp)
movl %r12d, 0x20(%rax)
movq %r15, 0x28(%rax)
xorl %eax, %eax
movl $0x0, %r12d
movl $0x0, %r15d
testq %r13, %r13
jne 0xdfb1
movq 0x58(%rsp), %rax
movq %rax, %r14
movq 0x60(%rsp), %r15
jmp 0xe05f
incq %r14
movq %r14, %rax
movq $0x0, (%r15)
addl $0x10000, %ebp          # imm = 0x10000
cmpq 0x50(%rsp), %rax
jne 0xdf7e
movq 0x20(%rsp), %r15
movq $0x0, 0x18(%rsp)
movq 0x28(%rsp), %rax
movl 0xc(%rax), %ebp
cmpb $0x0, 0x28(%rax)
movl $0x12c, %eax            # imm = 0x12C
movl $0x64, %r14d
cmovel %eax, %r14d
movq %r15, 0x8(%rsp)
testq %r15, %r15
je 0xe257
xorl %ebx, %ebx
movq %rbx, (%rsp)
movq 0x28(%r15), %rax
movq %rax, 0x40(%rsp)
movl $0x0, 0x20(%r15)
movq %rbx, 0x28(%r15)
movq (%r15), %r15
leaq 0x40(%rsp), %rdi
leaq 0x18f1(%rip), %rsi      # 0xf9c9
callq 0x201c4
movq 0x40(%rsp), %r12
testq %r12, %r12
je 0xe189
movl 0xc(%r12), %eax
xorl %ebx, %ebx
movq %r12, %r13
movl %eax, %ecx
addl %r14d, %ecx
movq (%r12), %r12
movl 0xc(%r13), %eax
cmpl %ecx, %eax
jbe 0xe172
cmpl 0x14(%rsp), %ebx
jge 0xe122
movq $0x0, (%rsp)
movq 0x8(%rsp), %rcx
movl $0x0, 0x20(%rcx)
jmp 0xe170
movq %rsp, %rdi
callq 0x20173
movq (%rsp), %rax
movq 0x8(%rsp), %rdi
movq %rax, 0x28(%rdi)
movq $0x0, (%rsp)
movl %ebx, 0x20(%rdi)
movl %ebp, %esi
callq 0xf9e9
movq 0x8(%rsp), %rdx
movq 0x28(%rsp), %rdi
leaq 0x18(%rsp), %rsi
callq 0xfa4d
movl $0x38, %edi
callq 0x2dff4
movq %rax, 0x8(%rsp)
movl 0xc(%r13), %eax
xorl %ebx, %ebx
movq (%rsp), %rcx
movq %rcx, (%r13)
movq %r13, (%rsp)
incl %ebx
testq %r12, %r12
jne 0xe0f2
movq %rsp, %rdi
callq 0x20173
movq (%rsp), %rax
movq 0x8(%rsp), %rdi
movq %rax, 0x28(%rdi)
cmpl 0x14(%rsp), %ebx
jge 0xe1b0
leaq 0x8(%rsp), %rdi
callq 0x2e0b0
jmp 0xe1ce
movl %ebx, 0x20(%rdi)
movl %ebp, %esi
callq 0xf9e9
movq 0x8(%rsp), %rdx
movq 0x28(%rsp), %rdi
leaq 0x18(%rsp), %rsi
callq 0xfa4d
movq %r15, 0x8(%rsp)
testq %r15, %r15
jne 0xe0ae
movq 0x18(%rsp), %rbx
movq %rbx, 0x20(%rsp)
testq %rbx, %rbx
movq 0x48(%rsp), %r12
je 0xe257
leaq 0x1995(%rip), %r15      # 0xfb8c
leaq 0x18(%rsp), %r14
movq 0x28(%rbx), %rax
movq %rax, 0x18(%rsp)
testq %rax, %rax
je 0xe24f
movq %r14, %rdi
movq %r15, %rsi
callq 0x201c4
movq 0x18(%rsp), %rcx
movl 0x8(%rcx), %esi
leal (%rsi,%r12), %edx
xorl %eax, %eax
movl 0x8(%rcx), %edi
cmpl %edx, %edi
jbe 0xe236
subl %esi, %edx
addl %edx, %eax
leal (%rdi,%r12), %edx
movl %edi, %esi
jmp 0xe240
addl %r12d, %edi
cmpl %edx, %edi
cmovbel %edx, %edi
movl %edi, %edx
movq (%rcx), %rcx
testq %rcx, %rcx
jne 0xe223
subl %esi, %eax
addl %edx, %eax
movl %eax, 0x30(%rbx)
movq (%rbx), %rbx
testq %rbx, %rbx
jne 0xe1fc
leaq 0x175e(%rip), %rsi      # 0xf9bc
leaq 0x20(%rsp), %rbx
movq %rbx, %rdi
callq 0x201c4
leaq 0x30(%rsp), %rdi
callq 0x2e0b0
movq (%rbx), %rax
addq $0x68, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq