// File: /workspace/github_c_makefile_star2_O1/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 $0x68, %rsp
movq %r9, 0x10(%rsp)
movl %r8d, 0xc(%rsp)
movl %ecx, %r15d
movl %edx, %ebp
movl %esi, %r13d
movq %rdi, %rbx
movl $0x12, %edi
movl $0x1, %esi
callq 0x29160
movq %rax, 0x18(%rsp)
movq %rbx, %r12
testq %rbx, %rbx
je 0xd724
leaq 0x80584(%rip), %r14     # 0x8dc6c
movq %r12, %rbx
movq 0x18(%rsp), %rdi
movq 0x8(%rbx), %rsi
callq 0x28b2c
testq %rax, %rax
je 0xd70c
movq 0x8(%rbx), %rsi
movq %r14, %rdi
xorl %eax, %eax
callq 0x26b6f
movq 0x18(%rsp), %rdi
movq 0x8(%rbx), %rsi
xorl %edx, %edx
callq 0x28dbe
movq (%rbx), %rbx
testq %rbx, %rbx
jne 0xd6eb
leaq 0x18(%rsp), %rdi
callq 0x29565
movl %r13d, %edi
movl %ebp, %esi
movl %r15d, %edx
movl 0xb8(%rsp), %ecx
movl 0xc(%rsp), %r8d
movq 0x10(%rsp), %r9
movl 0xa8(%rsp), %eax
pushq %rax
movl 0xa8(%rsp), %r14d
pushq %r14
callq 0xccd3
addq $0x10, %rsp
movq %rax, %r13
movl 0x2c(%rax), %ebx
movq %r12, %rdi
callq 0x1fbec
movl %eax, %ebp
testl %ebx, %ebx
jle 0xd7b6
testq %r12, %r12
je 0xd791
movq %r12, %r15
movq %r13, %rdi
movq %r15, %rsi
callq 0xf1ba
movq (%r15), %r15
testq %r15, %r15
jne 0xd77e
movq 0x38(%r13), %rbx
movslq 0x14(%r13), %r14
testq %r14, %r14
jle 0xd881
xorl %ecx, %ecx
xorl %eax, %eax
addl (%rbx,%rcx,4), %eax
incq %rcx
cmpq %rcx, %r14
jne 0xd7a6
jmp 0xd883
testl %r14d, %r14d
je 0xd7c3
movq %r13, %rdi
callq 0xd4b6
testq %r12, %r12
je 0xd7de
movq %r12, %r15
movq %r13, %rdi
movq %r15, %rsi
callq 0xf1ba
movq (%r15), %r15
testq %r15, %r15
jne 0xd7cb
movq %r13, %rdi
callq 0xce4f
movslq 0x14(%r13), %rax
testq %rax, %rax
jle 0xd80d
movq 0x38(%r13), %rcx
movl (%r13), %edx
xorl %esi, %esi
cmpl %edx, (%rcx,%rsi,4)
jae 0xd805
movl $0x0, (%rcx,%rsi,4)
incq %rsi
cmpq %rsi, %rax
jne 0xd7f9
testl %ebp, %ebp
jle 0xdad1
movl %ebp, %eax
shlq $0x3, %rax
leaq (%rax,%rax,4), %r15
movq %r15, %rdi
callq 0x2db04
movq %rax, 0x20(%r13)
movl %ebp, 0x1c(%r13)
xorl %ebx, %ebx
xorl %ebp, %ebp
movq %r13, %rdi
movq %r12, %rsi
movl %ebp, %edx
callq 0xcec9
movq 0x20(%r13), %r14
movq %r12, 0x10(%r14,%rbx)
movl %ebp, 0x18(%r14,%rbx)
addl 0x18(%r12), %ebp
movl %ebp, 0x1c(%r14,%rbx)
cmpl $0x0, 0xb0(%rsp)
je 0xd86f
movq %r12, %rdi
callq 0x24d6a
movq %rax, 0x20(%r14,%rbx)
movq (%r12), %r12
addq $0x28, %rbx
cmpq %rbx, %r15
jne 0xd833
jmp 0xdad7
xorl %eax, %eax
movq 0x50(%r13), %r15
testl %eax, %eax
jle 0xd89b
addl %eax, %eax
leal (%rax,%rax,2), %edi
callq 0x2dbbc
movq %rax, 0x40(%r13)
jmp 0xd89d
xorl %eax, %eax
testl %r14d, %r14d
jle 0xd8bc
xorl %ecx, %ecx
movslq (%rbx,%rcx,4), %rdx
movq %rax, (%r15,%rcx,8)
leaq (%rdx,%rdx,2), %rdx
leaq (%rax,%rdx,2), %rax
incq %rcx
cmpq %rcx, %r14
jne 0xd8a4
movslq 0x14(%r13), %rax
testq %rax, %rax
jle 0xd8e3
movq 0x38(%r13), %rcx
movl (%r13), %edx
xorl %esi, %esi
cmpl %edx, (%rcx,%rsi,4)
jae 0xd8db
movl $0x0, (%rcx,%rsi,4)
incq %rsi
cmpq %rsi, %rax
jne 0xd8cf
movslq %ebp, %rax
shlq $0x3, %rax
leaq (%rax,%rax,4), %rdi
callq 0x2db04
movq %rax, 0x20(%r13)
movl %ebp, 0x1c(%r13)
testl %ebp, %ebp
jle 0xda98
movl %ebp, %eax
movq %rax, 0x20(%rsp)
xorl %r14d, %r14d
movl $0x0, 0x8(%rsp)
movq %r13, 0x28(%rsp)
movq %r14, 0x30(%rsp)
movq 0x10(%r12), %r15
movslq 0x10(%r13), %rax
movq %rax, 0x58(%rsp)
movl 0xc(%r13), %eax
movl 0x2c(%r13), %ecx
movl %ecx, 0xc(%rsp)
cmpb $0x0, 0x28(%r13)
movq %r12, 0x38(%rsp)
movl 0x18(%r12), %ecx
movl %ecx, 0x10(%rsp)
leaq -0x116c(%rip), %rdx     # 0xc7e7
leaq -0x11a8(%rip), %rcx     # 0xc7b2
cmoveq %rcx, %rdx
movq %rdx, 0x60(%rsp)
movq 0x38(%r13), %rcx
movq %rcx, 0x48(%rsp)
movq 0x50(%r13), %rcx
movq %rcx, 0x40(%rsp)
cmpb $0x0, 0xb3620(%rip)     # 0xc0f9c
jne 0xd9ad
movl $0x2, 0xb218c(%rip)     # 0xbfb14
movl $0x1, 0xb218a(%rip)     # 0xbfb1c
movl $0x0, 0xb21c4(%rip)     # 0xbfb60
movl $0x3, 0xb2186(%rip)     # 0xbfb2c
movb $0x1, 0xb35ef(%rip)     # 0xc0f9c
subl %eax, 0x10(%rsp)
js 0xda39
subl 0xc(%rsp), %eax
cltq
movq %rax, 0x50(%rsp)
xorl %r14d, %r14d
movl 0x8(%rsp), %ebp
movq %r15, %rdi
movq 0x50(%rsp), %rbx
movl %ebx, %esi
movq 0x60(%rsp), %r12
callq *%r12
movl %eax, %r13d
leaq (%r15,%rbx), %rdi
movl 0xc(%rsp), %esi
callq *%r12
testl %r13d, %r13d
js 0xda25
testl %eax, %eax
js 0xda25
movl %r13d, %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)
leaq (%rsi,%rsi,2), %rcx
movw %ax, (%rdx,%rcx,2)
movl %ebp, %eax
shrl $0x10, %eax
movw %ax, 0x2(%rdx,%rcx,2)
movw %bp, 0x4(%rdx,%rcx,2)
movq 0x58(%rsp), %rax
addl %eax, %ebp
addq %rax, %r15
addl %eax, %r14d
cmpl 0x10(%rsp), %r14d
jle 0xd9c9
movq 0x28(%rsp), %r13
movq 0x20(%r13), %rax
movq 0x30(%rsp), %r14
leaq (%r14,%r14,4), %rcx
movq 0x38(%rsp), %r12
movq %r12, 0x10(%rax,%rcx,8)
movl 0x8(%rsp), %edx
movl %edx, 0x18(%rax,%rcx,8)
addl 0x18(%r12), %edx
movl %edx, 0x8(%rsp)
movl %edx, 0x1c(%rax,%rcx,8)
cmpl $0x0, 0xb0(%rsp)
je 0xda84
leaq (%rax,%rcx,8), %rbx
movq %r12, %rdi
callq 0x24d6a
movq %rax, 0x20(%rbx)
incq %r14
movq (%r12), %r12
cmpq 0x20(%rsp), %r14
jne 0xd91a
jmp 0xdaa0
movl $0x0, 0x8(%rsp)
movl 0x8(%rsp), %eax
movl %eax, 0x30(%r13)
movslq 0x14(%r13), %rax
testq %rax, %rax
jle 0xdb02
movq 0x38(%r13), %rcx
movl (%r13), %edx
xorl %esi, %esi
cmpl %edx, (%rcx,%rsi,4)
jb 0xdac7
movl $0x0, (%rcx,%rsi,4)
incq %rsi
cmpq %rsi, %rax
jne 0xdabb
jmp 0xdb02
movl %ebp, 0x1c(%r13)
xorl %ebp, %ebp
movl %ebp, 0x30(%r13)
movslq 0x14(%r13), %rax
testq %rax, %rax
jle 0xdb02
movq 0x38(%r13), %rcx
movl (%r13), %edx
xorl %esi, %esi
cmpl %edx, (%rcx,%rsi,4)
jb 0xdafa
movl $0x0, (%rcx,%rsi,4)
incq %rsi
cmpq %rsi, %rax
jne 0xdaee
movq %r13, %rax
addq $0x68, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq