// File: /workspace/github_c_makefile_star2_O2/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 0x55ce
leaq 0x11674(%rip), %rsi     # 0x16f0b
xorl %r15d, %r15d
pushq $0x2
popq %rdi
xorl %eax, %eax
callq 0x110f9
leaq 0x1167a(%rip), %rdi     # 0x16f25
callq 0xf4e4
testl %eax, %eax
je 0x58d1
leaq 0x1166a(%rip), %rdi     # 0x16f25
xorl %esi, %esi
callq 0xf201
movl 0x30(%r14), %esi
movq %rbx, %rdi
movq %rax, %rdx
callq 0x5278
movq %r14, 0x10(%rsp)
movl 0x30(%r14), %eax
movl %eax, 0xc(%rsp)
movq %rbx, 0x18(%rsp)
movq 0x8(%rbx), %rdi
callq 0x3d6d
movq %rax, %r14
xorl %eax, %eax
callq 0x9a0d
testl %ebp, %ebp
cmovlel %r15d, %ebp
movq %rax, (%rsp)
subl $0x1, %ebp
jb 0x5977
pushq $0x18
popq %rdi
callq 0xd87c
movq %rax, %rbx
movq %r14, %r12
pushq $0x1
popq %r13
testl %r15d, %r15d
je 0x593c
xorl %r13d, %r13d
cmpl 0xc(%rsp), %r15d
setl %r13b
movq 0x10(%rsp), %rdi
movq (%rsp), %rsi
callq 0x41fd
movq %rax, %r12
addl %r15d, %r13d
testq %r12, %r12
je 0x5977
movq 0x18(%r12), %r15
movq %r15, 0x10(%rbx)
movq (%rsp), %rdi
movq %rbx, %rsi
callq 0x9af7
movq %r12, %rdi
callq 0x426b
movq 0x14(%r15), %xmm0
paddd 0x106b4(%rip), %xmm0    # 0x16020
movq %xmm0, 0x14(%r15)
movl %r13d, %r15d
jmp 0x5900
movl 0x20ec3(%rip), %edx     # 0x26840
leaq 0x1182b(%rip), %rsi     # 0x171af
pushq $0x3
popq %rdi
xorl %eax, %eax
callq 0x110f9
leaq 0x117cc(%rip), %rsi     # 0x17161
pushq $0x2
popq %rdi
xorl %eax, %eax
callq 0x110f9
leaq 0x117da(%rip), %rdi     # 0x17180
xorl %esi, %esi
callq 0xf201
testq %rax, %rax
je 0x59fe
leaq 0x1207a(%rip), %rsi     # 0x17a33
movq %rax, %rdi
callq 0x8645
movq %rax, %rbx
movq %rax, 0x20(%rsp)
leaq 0x1227e(%rip), %r14     # 0x17c4e
movq (%rsp), %r15
movq (%r15), %r15
cmpq $0x0, (%r15)
je 0x59f4
movq 0x10(%r15), %rax
movq 0x8(%rax), %rdx
movq %rbx, %rdi
movq %r14, %rsi
xorl %eax, %eax
callq 0x3470
jmp 0x59d4
leaq 0x20(%rsp), %rdi
callq 0x8c9c
movq 0x10(%rsp), %r14
movq %r14, %rdi
movq (%rsp), %rsi
callq 0x4968
leaq 0x11773(%rip), %rsi     # 0x17189
pushq $0x2
popq %rdi
xorl %eax, %eax
callq 0x110f9
leaq 0x11504(%rip), %rdi     # 0x16f2b
callq 0xf4e4
testl %eax, %eax
movq 0x18(%rsp), %rbx
je 0x5a52
leaq 0x114ef(%rip), %rdi     # 0x16f2b
xorl %esi, %esi
callq 0xf201
movl 0x30(%r14), %esi
movq %rbx, %rdi
movq %rax, %rdx
callq 0x5278
movq (%rsp), %rax
addq $0x28, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq