// File: /workspace/github_c_makefile_star2_O0/icebert[P]pblat/jkOwnLib/gfBlatLib.c
// Function: gfAlignSomeClumps
static void gfAlignSomeClumps(struct genoFind *gf,  struct gfClump *clumpList, 
    bioSeq *seq, boolean isRc,  int minMatch, 
    struct gfOutput *out, boolean isProt, enum ffStringency stringency)
/* Convert gfClumps to an actual alignment that gets saved via 
 * outFunction/outData. */
{
struct gfClump *clump;
struct gfRange *rangeList = NULL, *range;
bioSeq *targetSeq;
struct ssBundle *bun;
int intronMax = ffIntronMax;

if (isProt)
    intronMax /= 3;
for (clump = clumpList; clump != NULL; clump = clump->next)
    {
    clumpToHspRange(clump, seq, gf->tileSize, 0, NULL, &rangeList, isProt, FALSE);
    }
slReverse(&rangeList);
slSort(&rangeList, gfRangeCmpTarget);
rangeList = gfRangesBundle(rangeList, intronMax);
for (range = rangeList; range != NULL; range = range->next)
    {
    targetSeq = range->tSeq;
    AllocVar(bun);
    bun->qSeq = seq;
    bun->genoSeq = targetSeq;
    bun->ffList = gfRangesToFfItem(range->components, seq);
    bun->isProt = isProt;
    ssStitch(bun, stringency, minMatch, ssAliCount);
    saveAlignments(targetSeq->name, targetSeq->size, 0, 
	bun, NULL, isRc, FALSE, stringency, minMatch, out);
    ssBundleFree(&bun);
    }
gfRangeFreeList(&rangeList);
}

// Assembly:
pushq %rbp
movq %rsp, %rbp
subq $0x80, %rsp
movl 0x18(%rbp), %eax
movl 0x10(%rbp), %eax
movq %rdi, -0x8(%rbp)
movq %rsi, -0x10(%rbp)
movq %rdx, -0x18(%rbp)
movl %ecx, -0x1c(%rbp)
movl %r8d, -0x20(%rbp)
movq %r9, -0x28(%rbp)
movq $0x0, -0x38(%rbp)
leaq 0xf4799(%rip), %rax     # 0x106ca0
movl (%rax), %eax
movl %eax, -0x54(%rbp)
cmpl $0x0, 0x10(%rbp)
je 0x12520
movl -0x54(%rbp), %eax
movl $0x3, %ecx
cltd
idivl %ecx
movl %eax, -0x54(%rbp)
movq -0x10(%rbp), %rax
movq %rax, -0x30(%rbp)
cmpq $0x0, -0x30(%rbp)
je 0x12567
movq -0x30(%rbp), %rdi
movq -0x18(%rbp), %rsi
movq -0x8(%rbp), %rax
movl 0xc(%rax), %edx
movl 0x10(%rbp), %eax
xorl %ecx, %ecx
xorl %r8d, %r8d
leaq -0x38(%rbp), %r9
movl %eax, (%rsp)
movl $0x0, 0x8(%rsp)
callq 0x12980
movq -0x30(%rbp), %rax
movq (%rax), %rax
movq %rax, -0x30(%rbp)
jmp 0x12528
leaq -0x38(%rbp), %rdi
callq 0x2aad0
leaq -0x38(%rbp), %rdi
leaq -0xd4b(%rip), %rsi      # 0x11830
callq 0x2ab90
movq -0x38(%rbp), %rdi
movl -0x54(%rbp), %esi
callq 0x119f0
movq %rax, -0x38(%rbp)
movq -0x38(%rbp), %rax
movq %rax, -0x40(%rbp)
cmpq $0x0, -0x40(%rbp)
je 0x1266c
movq -0x40(%rbp), %rax
movq 0x18(%rax), %rax
movq %rax, -0x48(%rbp)
movl $0x48, %edi
callq 0x40c50
movq %rax, -0x50(%rbp)
movq -0x18(%rbp), %rcx
movq -0x50(%rbp), %rax
movq %rcx, 0x10(%rax)
movq -0x48(%rbp), %rcx
movq -0x50(%rbp), %rax
movq %rcx, 0x18(%rax)
movq -0x40(%rbp), %rax
movq 0x28(%rax), %rdi
movq -0x18(%rbp), %rsi
callq 0x12370
movq %rax, %rcx
movq -0x50(%rbp), %rax
movq %rcx, 0x8(%rax)
movl 0x10(%rbp), %ecx
movq -0x50(%rbp), %rax
movl %ecx, 0x30(%rax)
movq -0x50(%rbp), %rdi
movl 0x18(%rbp), %esi
movl -0x20(%rbp), %edx
movl 0xf37e9(%rip), %ecx     # 0x105df4
callq 0x18b80
movq -0x48(%rbp), %rax
movq 0x8(%rax), %rdi
movq -0x48(%rbp), %rax
movl 0x18(%rax), %esi
movq -0x50(%rbp), %rcx
movl -0x1c(%rbp), %r9d
movl 0x18(%rbp), %r11d
movl -0x20(%rbp), %r10d
movq -0x28(%rbp), %rax
xorl %edx, %edx
xorl %r8d, %r8d
movl $0x0, (%rsp)
movl %r11d, 0x8(%rsp)
movl %r10d, 0x10(%rsp)
movq %rax, 0x18(%rsp)
callq 0x121d0
leaq -0x50(%rbp), %rdi
callq 0x183a0
movq -0x40(%rbp), %rax
movq (%rax), %rax
movq %rax, -0x40(%rbp)
jmp 0x12598
leaq -0x38(%rbp), %rdi
callq 0x117e0
addq $0x80, %rsp
popq %rbp
retq
nop