// File: /workspace/github_c_makefile_star2_O3/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, 0x18(%rsp)
movl %ecx, 0x4(%rsp)
movl %edx, %r12d
movl %esi, %r15d
movq %rdi, %rbx
movl $0x12, %edi
movl $0x1, %esi
callq 0x294ea
movq %rax, 0x60(%rsp)
movq %rbx, %r13
testq %rbx, %rbx
je 0xd7d6
movq %rax, %r14
leaq 0x8051e(%rip), %rbp     # 0x8dcbc
movq %r13, %rbx
movq 0x8(%rbx), %rsi
movq %r14, %rdi
callq 0x28eb0
testq %rax, %rax
je 0xd7c0
movq 0x8(%rbx), %rsi
movq %rbp, %rdi
xorl %eax, %eax
callq 0x26e94
movq 0x8(%rbx), %rsi
movq %r14, %rdi
xorl %edx, %edx
callq 0x29142
movq (%rbx), %rbx
testq %rbx, %rbx
jne 0xd7a1
leaq 0x60(%rsp), %rdi
callq 0x298bd
movl %r15d, %edi
movl %r12d, %esi
movl 0x4(%rsp), %edx
movl 0xb8(%rsp), %ecx
movl 0x18(%rsp), %r8d
movq 0x10(%rsp), %r9
movl 0xa8(%rsp), %eax
pushq %rax
movl 0xa8(%rsp), %r15d
pushq %r15
callq 0xcc67
addq $0x10, %rsp
movq %rax, %r14
movl 0x2c(%rax), %ebx
movq %r13, %rdi
callq 0x200ac
movl %eax, %ebp
testl %ebx, %ebx
movq %r14, 0x8(%rsp)
jle 0xd896
testq %r13, %r13
je 0xd84e
movq %r13, %rbx
movq 0x10(%rbx), %rsi
movl 0x18(%rbx), %edx
movq %r14, %rdi
callq 0xf2da
movq (%rbx), %rbx
testq %rbx, %rbx
jne 0xd837
movslq 0x14(%r14), %rbx
testq %rbx, %rbx
jle 0xd9b8
movq %r14, %rax
movq 0x38(%r14), %r14
movq 0x50(%rax), %r15
xorl %ecx, %ecx
xorl %eax, %eax
addl (%r14,%rcx,4), %eax
incq %rcx
cmpq %rcx, %rbx
jne 0xd86a
testl %eax, %eax
jle 0xd971
addl %eax, %eax
leal (%rax,%rax,2), %edi
callq 0x2df1b
movq 0x8(%rsp), %rcx
movq %rax, 0x40(%rcx)
jmp 0xd973
testl %r15d, %r15d
je 0xd8a3
movq %r14, %rdi
callq 0xd544
testq %r13, %r13
je 0xd8c2
movq %r13, %rbx
movq 0x10(%rbx), %rsi
movl 0x18(%rbx), %edx
movq %r14, %rdi
callq 0xf2da
movq (%rbx), %rbx
testq %rbx, %rbx
jne 0xd8ab
movq %r14, %rdi
callq 0xcec3
movq 0x38(%r14), %rax
movslq 0x14(%r14), %rcx
testq %rcx, %rcx
jle 0xd8f0
movl (%r14), %edx
xorl %esi, %esi
cmpl %edx, (%rax,%rsi,4)
jae 0xd8e8
movl $0x0, (%rax,%rsi,4)
incq %rsi
cmpq %rsi, %rcx
jne 0xd8dc
testl %ebp, %ebp
jle 0xdb9b
movl %ebp, %eax
shlq $0x3, %rax
leaq (%rax,%rax,4), %r15
movq %r15, %rdi
callq 0x2de63
movq %rax, 0x20(%r14)
movl %ebp, 0x1c(%r14)
xorl %ebx, %ebx
xorl %ebp, %ebp
movq 0x10(%r13), %rsi
movl 0x18(%r13), %edx
movq %r14, %rdi
movl %ebp, %ecx
callq 0xcf39
movq 0x20(%r14), %r14
movq %r13, 0x10(%r14,%rbx)
movl %ebp, 0x18(%r14,%rbx)
addl 0x18(%r13), %ebp
movl %ebp, 0x1c(%r14,%rbx)
cmpl $0x0, 0xb0(%rsp)
je 0xd956
movq %r13, %rdi
callq 0x25071
movq %rax, 0x20(%r14,%rbx)
movq (%r13), %r13
addq $0x28, %rbx
cmpq %rbx, %r15
movq 0x8(%rsp), %r14
jne 0xd916
movq 0x38(%r14), %rax
jmp 0xdba1
xorl %eax, %eax
xorl %ecx, %ecx
movslq (%r14,%rcx,4), %rdx
movq %rax, (%r15,%rcx,8)
leaq (%rdx,%rdx,2), %rdx
leaq (%rax,%rdx,2), %rax
incq %rcx
cmpq %rcx, %rbx
jne 0xd975
movq 0x8(%rsp), %r14
movslq 0x14(%r14), %rax
testq %rax, %rax
jle 0xd9b8
movq 0x38(%r14), %rcx
movl (%r14), %edx
xorl %esi, %esi
cmpl %edx, (%rcx,%rsi,4)
jae 0xd9b0
movl $0x0, (%rcx,%rsi,4)
incq %rsi
cmpq %rsi, %rax
jne 0xd9a4
movslq %ebp, %rax
shlq $0x3, %rax
leaq (%rax,%rax,4), %rdi
callq 0x2de63
movq %rax, 0x20(%r14)
movl %ebp, 0x1c(%r14)
testl %ebp, %ebp
jle 0xdb6c
movl %ebp, %eax
movq %rax, 0x28(%rsp)
xorl %ebp, %ebp
xorl %edx, %edx
movq 0x10(%r13), %r15
movl 0x18(%r13), %r12d
movslq 0x10(%r14), %rax
movq %rax, 0x58(%rsp)
movl 0xc(%r14), %eax
cmpb $0x0, 0x28(%r14)
movl 0x2c(%r14), %ecx
movl %ecx, 0x10(%rsp)
leaq -0x12a2(%rip), %rsi     # 0xc76a
leaq -0x12de(%rip), %rcx     # 0xc735
cmoveq %rcx, %rsi
movq %rsi, 0x18(%rsp)
movq 0x38(%r14), %rcx
movq %rcx, 0x48(%rsp)
movq 0x50(%r14), %rcx
movq %rcx, 0x40(%rsp)
cmpb $0x0, 0xb3567(%rip)     # 0xc0f9c
jne 0xda66
movl $0x2, 0xb20d3(%rip)     # 0xbfb14
movl $0x1, 0xb20d1(%rip)     # 0xbfb1c
movl $0x0, 0xb210b(%rip)     # 0xbfb60
movl $0x3, 0xb20cd(%rip)     # 0xbfb2c
movb $0x1, 0xb3536(%rip)     # 0xc0f9c
movl %r12d, %ecx
subl %eax, %ecx
movl %ecx, 0x4(%rsp)
js 0xdb1b
movq %rbp, 0x30(%rsp)
movq %r13, 0x38(%rsp)
subl 0x10(%rsp), %eax
cltq
movq %rax, 0x50(%rsp)
xorl %ebp, %ebp
movl %edx, 0x24(%rsp)
movl %edx, %r14d
movq %r15, %rdi
movq 0x50(%rsp), %rbx
movl %ebx, %esi
movq 0x18(%rsp), %r12
callq *%r12
movl %eax, %r13d
leaq (%r15,%rbx), %rdi
movl 0x10(%rsp), %esi
callq *%r12
testl %r13d, %r13d
js 0xdaf1
testl %eax, %eax
js 0xdaf1
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 %r14d, %eax
shrl $0x10, %eax
movw %ax, 0x2(%rdx,%rcx,2)
movw %r14w, 0x4(%rdx,%rcx,2)
movq 0x58(%rsp), %rax
addl %eax, %r14d
addq %rax, %r15
addl %eax, %ebp
cmpl 0x4(%rsp), %ebp
jle 0xda93
movq 0x38(%rsp), %r13
movl 0x18(%r13), %r12d
movq 0x8(%rsp), %r14
movq 0x30(%rsp), %rbp
movl 0x24(%rsp), %edx
addl %edx, %r12d
movq 0x20(%r14), %rax
leaq (,%rbp,4), %rcx
addq %rbp, %rcx
movq %r13, 0x10(%rax,%rcx,8)
movl %edx, 0x18(%rax,%rcx,8)
movl %r12d, 0x1c(%rax,%rcx,8)
cmpl $0x0, 0xb0(%rsp)
je 0xdb55
leaq (%rax,%rcx,8), %rbx
movq %r13, %rdi
callq 0x25071
movq %rax, 0x20(%rbx)
incq %rbp
movq (%r13), %r13
movl %r12d, %edx
cmpq 0x28(%rsp), %rbp
jne 0xd9e3
jmp 0xdb6f
xorl %r12d, %r12d
movl %r12d, 0x30(%r14)
movslq 0x14(%r14), %rax
testq %rax, %rax
jle 0xdbc7
movq 0x38(%r14), %rcx
movl (%r14), %edx
xorl %esi, %esi
cmpl %edx, (%rcx,%rsi,4)
jb 0xdb91
movl $0x0, (%rcx,%rsi,4)
incq %rsi
cmpq %rsi, %rax
jne 0xdb85
jmp 0xdbc7
movl %ebp, 0x1c(%r14)
xorl %ebp, %ebp
movl %ebp, 0x30(%r14)
movslq 0x14(%r14), %rcx
testq %rcx, %rcx
jle 0xdbc7
movl (%r14), %edx
xorl %esi, %esi
cmpl %edx, (%rax,%rsi,4)
jb 0xdbbf
movl $0x0, (%rax,%rsi,4)
incq %rsi
cmpq %rsi, %rcx
jne 0xdbb3
movq %r14, %rax
addq $0x68, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq