// File: /workspace/github_c_makefile_star2_O0/icebert[P]pblat/jkOwnLib/ffSeedExtend.c
// Function: refineBundle
static void refineBundle(struct genoFind *gf, 
	struct dnaSeq *qSeq,  Bits *qMaskBits, int qMaskOffset,
	struct dnaSeq *tSeq, struct lm *lm, struct ssBundle *bun, boolean isRc)
/* Refine bundle - extending alignments and looking for smaller exons. */
{
struct ssFfItem *ffi;
struct gfSeqSource *target = gfFindNamedSource(gf, tSeq->name);

/* First do gapless expansions and restitch. */
for (ffi = bun->ffList; ffi != NULL; ffi = ffi->next)
    {
    ffi->ff = expandGapless(qSeq, tSeq, ffi->ff);
    }
ssStitch(bun, ffCdna, 16, 16);

for (ffi = bun->ffList; ffi != NULL; ffi = ffi->next)
    {
    ffi->ff = scanIndexForSmallExons(gf, target, qSeq, qMaskBits, qMaskOffset, 
	tSeq, lm, ffi->ff);
    ffi->ff = bandedExtend(qSeq, tSeq, ffi->ff);
    ffi->ff = scanForSmallerExons(gf->tileSize, qSeq, tSeq, isRc, ffi->ff);
    ffi->ff = refineSpliceSites(qSeq, tSeq, ffi->ff);
    ffi->ff = scanForTinyInternal(qSeq, tSeq, isRc, ffi->ff);
    ffi->ff = smoothSmallGaps(qSeq, tSeq, ffi->ff);
    ffi->ff = trimFlakyEnds(qSeq, tSeq, ffi->ff);
    }
}

// Assembly:
pushq %rbp
movq %rsp, %rbp
subq $0x50, %rsp
movl 0x18(%rbp), %eax
movq 0x10(%rbp), %rax
movq %rdi, -0x8(%rbp)
movq %rsi, -0x10(%rbp)
movq %rdx, -0x18(%rbp)
movl %ecx, -0x1c(%rbp)
movq %r8, -0x28(%rbp)
movq %r9, -0x30(%rbp)
movq -0x8(%rbp), %rdi
movq -0x28(%rbp), %rax
movq 0x8(%rax), %rsi
callq 0xf640
movq %rax, -0x40(%rbp)
movq 0x10(%rbp), %rax
movq 0x8(%rax), %rax
movq %rax, -0x38(%rbp)
cmpq $0x0, -0x38(%rbp)
je 0x1c1bb
movq -0x10(%rbp), %rdi
movq -0x28(%rbp), %rsi
movq -0x38(%rbp), %rax
movq 0x8(%rax), %rdx
callq 0x1cc50
movq %rax, %rcx
movq -0x38(%rbp), %rax
movq %rcx, 0x8(%rax)
movq -0x38(%rbp), %rax
movq (%rax), %rax
movq %rax, -0x38(%rbp)
jmp 0x1c187
movq 0x10(%rbp), %rdi
movl $0x1, %esi
movl $0x10, %ecx
movl %ecx, %edx
callq 0x18b80
movq 0x10(%rbp), %rax
movq 0x8(%rax), %rax
movq %rax, -0x38(%rbp)
cmpq $0x0, -0x38(%rbp)
je 0x1c301
movq -0x8(%rbp), %rdi
movq -0x40(%rbp), %rsi
movq -0x10(%rbp), %rdx
movq -0x18(%rbp), %rcx
movl -0x1c(%rbp), %r8d
movq -0x28(%rbp), %r9
movq -0x30(%rbp), %r10
movq -0x38(%rbp), %rax
movq 0x8(%rax), %rax
movq %r10, (%rsp)
movq %rax, 0x8(%rsp)
callq 0x1cde0
movq %rax, %rcx
movq -0x38(%rbp), %rax
movq %rcx, 0x8(%rax)
movq -0x10(%rbp), %rdi
movq -0x28(%rbp), %rsi
movq -0x38(%rbp), %rax
movq 0x8(%rax), %rdx
callq 0x1d1e0
movq %rax, %rcx
movq -0x38(%rbp), %rax
movq %rcx, 0x8(%rax)
movq -0x8(%rbp), %rax
movl 0xc(%rax), %edi
movq -0x10(%rbp), %rsi
movq -0x28(%rbp), %rdx
movl 0x18(%rbp), %ecx
movq -0x38(%rbp), %rax
movq 0x8(%rax), %r8
callq 0x1d370
movq %rax, %rcx
movq -0x38(%rbp), %rax
movq %rcx, 0x8(%rax)
movq -0x10(%rbp), %rdi
movq -0x28(%rbp), %rsi
movq -0x38(%rbp), %rax
movq 0x8(%rax), %rdx
callq 0x1d500
movq %rax, %rcx
movq -0x38(%rbp), %rax
movq %rcx, 0x8(%rax)
movq -0x10(%rbp), %rdi
movq -0x28(%rbp), %rsi
movl 0x18(%rbp), %edx
movq -0x38(%rbp), %rax
movq 0x8(%rax), %rcx
callq 0x1d620
movq %rax, %rcx
movq -0x38(%rbp), %rax
movq %rcx, 0x8(%rax)
movq -0x10(%rbp), %rdi
movq -0x28(%rbp), %rsi
movq -0x38(%rbp), %rax
movq 0x8(%rax), %rdx
callq 0x1d700
movq %rax, %rcx
movq -0x38(%rbp), %rax
movq %rcx, 0x8(%rax)
movq -0x10(%rbp), %rdi
movq -0x28(%rbp), %rsi
movq -0x38(%rbp), %rax
movq 0x8(%rax), %rdx
callq 0x1d7a0
movq %rax, %rcx
movq -0x38(%rbp), %rax
movq %rcx, 0x8(%rax)
movq -0x38(%rbp), %rax
movq (%rax), %rax
movq %rax, -0x38(%rbp)
jmp 0x1c1dc
addq $0x50, %rsp
popq %rbp
retq
nopw (%rax,%rax)