// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/jkOwnLib/genoFind.c
// Function: gfIndexSeq
struct genoFind *gfIndexSeq(bioSeq *seqList,
	int minMatch, int maxGap, int tileSize, int maxPat, char *oocFile, 
	boolean isPep, boolean allowOneMismatch, boolean maskUpper,
	int stepSize)
/* Make index for all seqs in list.  For DNA sequences upper case bits will
 * be unindexed. */
{
checkUniqueNames(seqList);
struct genoFind *gf = gfNewEmpty(minMatch, maxGap, tileSize, stepSize, maxPat, 
				oocFile, isPep, allowOneMismatch);
if (stepSize == 0)
    stepSize = tileSize;
if (gf->segSize > 0)
    {
    gfLargeIndexSeq(gf, seqList, minMatch, maxGap, tileSize, maxPat, oocFile, isPep, maskUpper);
    }
else
    {
    gfSmallIndexSeq(gf, seqList, minMatch, maxGap, tileSize, maxPat, oocFile, isPep, maskUpper);
    }
return gf;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x58, %rsp
movq %r9, 0x10(%rsp)
movl %r8d, 0x8(%rsp)
movl %ecx, 0x4(%rsp)
movl %edx, %r15d
movl %esi, %r13d
movq %rdi, %rbx
pushq $0x12
popq %rdi
pushq $0x1
popq %rsi
callq 0x245c9
movq %rax, %r14
movq %rax, 0x50(%rsp)
leaq 0x7152e(%rip), %rbp     # 0x7cc4c
movq %rbx, %r12
testq %rbx, %rbx
je 0xb758
movq 0x8(%rbx), %rsi
movq %r14, %rdi
callq 0x24088
testq %rax, %rax
je 0xb745
movq 0x8(%rbx), %rsi
movq %rbp, %rdi
xorl %eax, %eax
callq 0x223fb
movq 0x8(%rbx), %rsi
movq %r14, %rdi
xorl %edx, %edx
callq 0x242d0
movq (%rbx), %rbx
jmp 0xb721
leaq 0x50(%rsp), %rdi
callq 0x2494c
movl %r13d, %edi
movl %r15d, %esi
movl 0x4(%rsp), %edx
movl 0xa8(%rsp), %ecx
movl 0x8(%rsp), %r8d
movq 0x10(%rsp), %r9
movl 0x98(%rsp), %eax
pushq %rax
movl 0x98(%rsp), %r14d
pushq %r14
callq 0xae1c
popq %rcx
popq %rdx
movq %rax, %r13
movl 0x2c(%rax), %ebx
movq %r12, %rdi
callq 0x1c4aa
movl %eax, %ebp
testl %ebx, %ebx
jle 0xb7ff
movq %r12, %r15
testq %r15, %r15
je 0xb7c2
movq %r13, %rdi
movq %r15, %rsi
callq 0xcf26
movq (%r15), %r15
jmp 0xb7ad
movq 0x38(%r13), %rbx
movq 0x50(%r13), %r14
movl 0x14(%r13), %r15d
xorl %eax, %eax
testl %r15d, %r15d
cmovlel %eax, %r15d
xorl %ecx, %ecx
cmpq %rax, %r15
je 0xb7e6
addl (%rbx,%rax,4), %ecx
incq %rax
jmp 0xb7d9
testl %ecx, %ecx
jle 0xb8a4
imull $0x6, %ecx, %edi
callq 0x28ad7
movq %rax, 0x40(%r13)
jmp 0xb8a6
testl %r14d, %r14d
je 0xb80c
movq %r13, %rdi
callq 0xb4f2
movq %r12, %r15
movq %r13, %rdi
testq %r15, %r15
je 0xb824
movq %r15, %rsi
callq 0xcf26
movq (%r15), %r15
jmp 0xb80f
callq 0xaf4f
movq %r13, %rdi
callq 0xafc6
testl %ebp, %ebp
jle 0xb844
movl %ebp, %eax
imulq $0x28, %rax, %rdi
callq 0x28a1f
movq %rax, 0x20(%r13)
movl %ebp, 0x1c(%r13)
xorl %ebx, %ebx
testl %ebp, %ebp
cmovlel %ebx, %ebp
imulq $0x28, %rbp, %r14
xorl %ebp, %ebp
cmpq %rbx, %r14
je 0xba35
movq %r13, %rdi
movq %r12, %rsi
movl %ebp, %edx
callq 0xafea
movq 0x20(%r13), %r15
movq %r12, 0x10(%r15,%rbx)
movl %ebp, 0x18(%r15,%rbx)
addl 0x18(%r12), %ebp
movl %ebp, 0x1c(%r15,%rbx)
cmpl $0x0, 0xa0(%rsp)
je 0xb89a
movq %r12, %rdi
callq 0x209d5
movq %rax, 0x20(%r15,%rbx)
movq (%r12), %r12
addq $0x28, %rbx
jmp 0xb855
xorl %eax, %eax
xorl %ecx, %ecx
cmpq %rcx, %r15
je 0xb8c1
movslq (%rbx,%rcx,4), %rdx
movq %rax, (%r14,%rcx,8)
imulq $0x6, %rdx, %rdx
addq %rdx, %rax
incq %rcx
jmp 0xb8a8
movq %r13, %rdi
callq 0xafc6
movslq %ebp, %rax
imulq $0x28, %rax, %rdi
callq 0x28a1f
movq %rax, 0x20(%r13)
movl %ebp, 0x1c(%r13)
xorl %r14d, %r14d
testl %ebp, %ebp
cmovlel %r14d, %ebp
movl $0x0, (%rsp)
movq %r13, 0x28(%rsp)
movq %rbp, 0x20(%rsp)
cmpq %rbp, %r14
je 0xba32
movq %r14, 0x30(%rsp)
movq 0x10(%r12), %r15
movslq 0x10(%r13), %r14
movl 0xc(%r13), %ebp
movl 0x2c(%r13), %eax
movq %r12, 0x38(%rsp)
movl 0x18(%r12), %ecx
subl %ebp, %ecx
movl %ecx, 0x10(%rsp)
movl %eax, 0x1c(%rsp)
subl %eax, %ebp
cmpb $0x0, 0x28(%r13)
leaq -0xf52(%rip), %rbx      # 0xa9e6
leaq -0xf8b(%rip), %rax      # 0xa9b4
cmoveq %rax, %rbx
movq 0x38(%r13), %rax
movq %rax, 0x48(%rsp)
movq 0x50(%r13), %rax
movq %rax, 0x40(%rsp)
callq 0xd4c6
movl %ebp, 0x4(%rsp)
movslq %ebp, %r13
movq %r15, 0x8(%rsp)
addq %r15, %r13
xorl %ebp, %ebp
movl (%rsp), %r12d
cmpl 0x10(%rsp), %ebp
jg 0xb9d9
movq 0x8(%rsp), %rax
leaq (%rax,%rbp), %rdi
movl 0x4(%rsp), %esi
callq *%rbx
movl %eax, %r15d
movq %r13, %rdi
addq %rbp, %rdi
movl 0x1c(%rsp), %esi
callq *%rbx
testl %r15d, %r15d
js 0xb9d1
testl %eax, %eax
js 0xb9d1
movl %r15d, %ecx
movq 0x40(%rsp), %rdx
movq (%rdx,%rcx,8), %rdx
movq 0x48(%rsp), %r8
movslq (%r8,%rcx,4), %rsi
leal 0x1(%rsi), %edi
movl %edi, (%r8,%rcx,4)
imulq $0x6, %rsi, %rcx
movw %ax, (%rdx,%rcx)
movl %r12d, %eax
shrl $0x10, %eax
movw %ax, 0x2(%rdx,%rcx)
movw %r12w, 0x4(%rdx,%rcx)
addl %r14d, %r12d
addq %r14, %rbp
jmp 0xb96f
movq 0x28(%rsp), %r13
movq 0x20(%r13), %rbx
movq 0x30(%rsp), %r14
imulq $0x28, %r14, %rax
movq 0x38(%rsp), %r12
movq %r12, 0x10(%rbx,%rax)
movl (%rsp), %ecx
movl %ecx, 0x18(%rbx,%rax)
addl 0x18(%r12), %ecx
movl %ecx, (%rsp)
movl %ecx, 0x1c(%rbx,%rax)
cmpl $0x0, 0xa0(%rsp)
je 0xba21
addq %rax, %rbx
movq %r12, %rdi
callq 0x209d5
movq %rax, 0x20(%rbx)
incq %r14
movq (%r12), %r12
movq 0x20(%rsp), %rbp
jmp 0xb8f7
movl (%rsp), %ebp
movl %ebp, 0x30(%r13)
movq %r13, %rdi
callq 0xb09c
movq %r13, %rax
addq $0x58, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq