// File: /workspace/github_c_makefile_star2_O0/icebert[P]pblat/jkOwnLib/ffSeedExtend.c
// Function: ffSeedExtInMem
struct ssBundle *ffSeedExtInMem(struct genoFind *gf, struct dnaSeq *qSeq, Bits *qMaskBits, 
	int qOffset, struct lm *lm, int minScore, boolean isRc)
/* Do seed and extend type alignment */
{
struct ssBundle *bunList = NULL, *bun;
int hitCount;
struct gfClump *clumpList, *clump;
struct gfRange *rangeList = NULL, *range;
struct dnaSeq *tSeq;

clumpList = gfFindClumpsWithQmask(gf, qSeq, qMaskBits, qOffset, lm, &hitCount);
for (clump = clumpList; clump != NULL; clump = clump->next)
    clumpToExactRange(clump, qSeq, gf->tileSize, 0, NULL, &rangeList);
slSort(&rangeList, gfRangeCmpTarget);
rangeList = gfRangesBundle(rangeList, ffIntronMax);
for (range = rangeList; range != NULL; range = range->next)
    {
    range->qStart += qOffset;
    range->qEnd += qOffset;
    tSeq = range->tSeq;
    AllocVar(bun);
    bun->qSeq = qSeq;
    bun->genoSeq = tSeq;
    bun->ffList = gfRangesToFfItem(range->components, qSeq);
    bun->isProt = FALSE;
    bun->avoidFuzzyFindKludge = TRUE;
    ssStitch(bun, ffCdna, 16, 10);
    refineBundle(gf, qSeq, qMaskBits, qOffset, tSeq, lm, bun, isRc);
    slAddHead(&bunList, bun);
    }
gfRangeFreeList(&rangeList);
gfClumpFreeList(&clumpList);
return bunList;
}

// Assembly:
pushq %rbp
movq %rsp, %rbp
subq $0x80, %rsp
movl 0x10(%rbp), %eax
movq %rdi, -0x8(%rbp)
movq %rsi, -0x10(%rbp)
movq %rdx, -0x18(%rbp)
movl %ecx, -0x1c(%rbp)
movq %r8, -0x28(%rbp)
movl %r9d, -0x2c(%rbp)
movq $0x0, -0x38(%rbp)
movq $0x0, -0x60(%rbp)
movq -0x8(%rbp), %rdi
movq -0x10(%rbp), %rsi
movq -0x18(%rbp), %rdx
movl -0x1c(%rbp), %ecx
movq -0x28(%rbp), %r8
leaq -0x44(%rbp), %r9
callq 0xea60
movq %rax, -0x50(%rbp)
movq -0x50(%rbp), %rax
movq %rax, -0x58(%rbp)
cmpq $0x0, -0x58(%rbp)
je 0x1bcd0
movq -0x58(%rbp), %rdi
movq -0x10(%rbp), %rsi
movq -0x8(%rbp), %rax
movl 0xc(%rax), %edx
xorl %ecx, %ecx
xorl %eax, %eax
movl %eax, %r8d
leaq -0x60(%rbp), %r9
callq 0x1be10
movq -0x58(%rbp), %rax
movq (%rax), %rax
movq %rax, -0x58(%rbp)
jmp 0x1bc9d
leaq -0x60(%rbp), %rdi
leaq -0xa4ab(%rip), %rsi     # 0x11830
callq 0x2ab90
movq -0x60(%rbp), %rdi
leaq 0xeafb5(%rip), %rax     # 0x106ca0
movl (%rax), %esi
callq 0x119f0
movq %rax, -0x60(%rbp)
movq -0x60(%rbp), %rax
movq %rax, -0x68(%rbp)
cmpq $0x0, -0x68(%rbp)
je 0x1bde7
movl -0x1c(%rbp), %ecx
movq -0x68(%rbp), %rax
addl 0x8(%rax), %ecx
movl %ecx, 0x8(%rax)
movl -0x1c(%rbp), %ecx
movq -0x68(%rbp), %rax
addl 0xc(%rax), %ecx
movl %ecx, 0xc(%rax)
movq -0x68(%rbp), %rax
movq 0x18(%rax), %rax
movq %rax, -0x70(%rbp)
movl $0x48, %edi
callq 0x40c50
movq %rax, -0x40(%rbp)
movq -0x10(%rbp), %rcx
movq -0x40(%rbp), %rax
movq %rcx, 0x10(%rax)
movq -0x70(%rbp), %rcx
movq -0x40(%rbp), %rax
movq %rcx, 0x18(%rax)
movq -0x68(%rbp), %rax
movq 0x28(%rax), %rdi
movq -0x10(%rbp), %rsi
callq 0x12370
movq %rax, %rcx
movq -0x40(%rbp), %rax
movq %rcx, 0x8(%rax)
movq -0x40(%rbp), %rax
movl $0x0, 0x30(%rax)
movq -0x40(%rbp), %rax
movl $0x1, 0x40(%rax)
movq -0x40(%rbp), %rdi
movl $0x1, %esi
movl $0x10, %edx
movl $0xa, %ecx
callq 0x18b80
movq -0x8(%rbp), %rdi
movq -0x10(%rbp), %rsi
movq -0x18(%rbp), %rdx
movl -0x1c(%rbp), %ecx
movq -0x70(%rbp), %r8
movq -0x28(%rbp), %r9
movq -0x40(%rbp), %r10
movl 0x10(%rbp), %eax
movq %r10, (%rsp)
movl %eax, 0x8(%rsp)
callq 0x1c140
movq -0x40(%rbp), %rsi
leaq -0x38(%rbp), %rdi
callq 0x1c310
movq -0x68(%rbp), %rax
movq (%rax), %rax
movq %rax, -0x68(%rbp)
jmp 0x1bcfe
leaq -0x60(%rbp), %rdi
callq 0x117e0
leaq -0x50(%rbp), %rdi
callq 0xe5f0
movq -0x38(%rbp), %rax
addq $0x80, %rsp
popq %rbp
retq
nopw %cs:(%rax,%rax)