// File: /workspace/github_c_makefile_star2_O3/JimKent[P]linearSat/linearSat/linearSat.c
// Function: linearSatOneSize
struct dlList *linearSatOneSize(struct alphaStore *store, int outSize)
/* linearSat - assemble alpha repeat regions such as centromeres from reads that have
 * been parsed into various repeat monomer variants.  Cycles of these variants tend to
 * form higher order repeats. Returns list of outSize monomers. */
{
struct wordTree *wt = store->markovChains;
alphaStoreNormalize(store, outSize);
verbose(2, "Normalized Markov Chains\n");

if (optionExists("chain"))
    {
    char *fileName = optionVal("chain", NULL);
    wordTreeWrite(wt, store->maxChainSize, fileName);
    }

struct dlList *ll = wordTreeMakeList(store, store->maxChainSize, 
    pickWeightedRandomFromList(wt->children), outSize);

if (optionExists("afterChain"))
    {
    char *fileName = optionVal("afterChain", NULL);
    wordTreeWrite(wt, store->maxChainSize, fileName);
    }

return ll;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x28, %rsp
movl %esi, %ebp
movq %rdi, %r14
movq 0x20(%rdi), %rbx
callq 0x5a87
leaq 0x13186(%rip), %rsi     # 0x18f0b
movl $0x2, %edi
xorl %eax, %eax
callq 0x12a31
leaq 0x1318d(%rip), %rdi     # 0x18f25
callq 0x10d0b
testl %eax, %eax
je 0x5dbe
leaq 0x1317d(%rip), %rdi     # 0x18f25
xorl %esi, %esi
callq 0x10a3c
movl 0x30(%r14), %esi
movq %rbx, %rdi
movq %rax, %rdx
callq 0x56fd
movq %r14, 0x8(%rsp)
movl 0x30(%r14), %eax
movl %eax, 0x4(%rsp)
movq %rbx, 0x10(%rsp)
movq 0x8(%rbx), %rdi
callq 0x3fc2
movq %rax, 0x18(%rsp)
xorl %r14d, %r14d
xorl %eax, %eax
callq 0xa904
movq %rax, %r15
testl %ebp, %ebp
jle 0x5e62
movl $0x18, %edi
callq 0xee10
movq %rax, %r13
testl %r14d, %r14d
je 0x5e20
xorl %ebx, %ebx
cmpl 0x4(%rsp), %r14d
setl %bl
movq 0x8(%rsp), %rdi
movq %r15, %rsi
callq 0x44eb
movq %rax, %r12
addl %ebx, %r14d
jmp 0x5e2b
movl $0x1, %r14d
movq 0x18(%rsp), %r12
testq %r12, %r12
je 0x5e62
movq 0x18(%r12), %rbx
movq %rbx, 0x10(%r13)
movq %r15, %rdi
movq %r13, %rsi
callq 0xa9f5
movq %r12, %rdi
callq 0x456a
movq 0x14(%rbx), %xmm0
paddd 0x121c7(%rip), %xmm0    # 0x18020
movq %xmm0, 0x14(%rbx)
decl %ebp
jne 0x5def
movl 0x219b8(%rip), %edx     # 0x27820
leaq 0x13340(%rip), %rsi     # 0x191af
movl $0x3, %edi
xorl %eax, %eax
callq 0x12a31
leaq 0x132df(%rip), %rsi     # 0x19161
movl $0x2, %edi
xorl %eax, %eax
callq 0x12a31
leaq 0x132eb(%rip), %rdi     # 0x19180
xorl %esi, %esi
callq 0x10a3c
testq %rax, %rax
je 0x5ef0
leaq 0x13b8b(%rip), %rsi     # 0x19a33
movq %rax, %rdi
callq 0x932b
movq %rax, 0x20(%rsp)
movq (%r15), %r14
cmpq $0x0, (%r14)
je 0x5ee6
movq %rax, %r12
leaq 0x13d86(%rip), %rbx     # 0x19c4e
movq 0x10(%r14), %rax
movq 0x8(%rax), %rdx
movq %r12, %rdi
movq %rbx, %rsi
xorl %eax, %eax
callq 0x3470
movq (%r14), %r14
cmpq $0x0, (%r14)
jne 0x5ec8
leaq 0x20(%rsp), %rdi
callq 0x99bb
movq 0x8(%rsp), %rbx
movq %rbx, %rdi
movq %r15, %rsi
callq 0x4d1f
leaq 0x13282(%rip), %rsi     # 0x19189
movl $0x2, %edi
xorl %eax, %eax
callq 0x12a31
leaq 0x13011(%rip), %rdi     # 0x18f2b
callq 0x10d0b
testl %eax, %eax
je 0x5f41
leaq 0x13001(%rip), %rdi     # 0x18f2b
xorl %esi, %esi
callq 0x10a3c
movl 0x30(%rbx), %esi
movq 0x10(%rsp), %rdi
movq %rax, %rdx
callq 0x56fd
movq %r15, %rax
addq $0x28, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq