LLM4Binary/decompile-bench-makefile huggingface dataset:
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/lib/bits.c
// Function: bitFind
int bitFind(Bits *b, int startIx, boolean val, int bitCount)
/* Find the index of the the next set bit. */
{
unsigned char notByteVal = val ? 0 : 0xff;
int iBit = startIx;
int endByte = ((bitCount-1)>>3);
int iByte;

/* scan initial byte */
while (((iBit & 7) != 0) && (iBit < bitCount))
    {
    if (bitReadOne(b, iBit) == val)
        return iBit;
    iBit++;
    }

/* scan byte at a time, if not already in last byte */
iByte = (iBit >> 3);
if (iByte < endByte)
    {
    while ((iByte < endByte) && (b[iByte] == notByteVal))
        iByte++;
    iBit = iByte << 3;
    }

/* scan last byte */
while (iBit < bitCount)
    {
    if (bitReadOne(b, iBit) == val)
        return iBit;
    iBit++;
    }
 return bitCount;  /* not found */
}

// Assembly:
movl %ecx, %eax
leal -0x1(%rax), %r8d
sarl $0x3, %r8d
leaq 0x65578(%rip), %rcx     # 0x7dba6
movl %esi, %r9d
sarl $0x3, %r9d
movslq %r9d, %r10
cmpl %eax, %esi
jge 0x1865d
movl %esi, %r11d
andl $0x7, %r11d
je 0x1865d
movb (%r11,%rcx), %r9b
xorl %r11d, %r11d
testb %r9b, (%rdi,%r10)
setne %r11b
cmpl %edx, %r11d
je 0x1868f
incl %esi
jmp 0x1862e
pushq %rbp
pushq %rbx
cmpl %r8d, %r9d
jge 0x186c8
xorl %esi, %esi
testl %edx, %edx
movl $0xff, %r11d
cmovnel %esi, %r11d
movslq %r8d, %rbx
subq %r10, %rbx
addq %rdi, %r10
cmpq %rsi, %rbx
je 0x18698
movzbl (%r10,%rsi), %ebp
cmpl %ebp, %r11d
jne 0x18692
incq %rsi
jmp 0x1867b
movl %esi, %eax
retq
addl %esi, %r9d
movl %r9d, %r8d
shll $0x3, %r8d
movl %r8d, %esi
jmp 0x186c8
movl %esi, %r8d
sarl $0x3, %r8d
movslq %r8d, %r8
movl %esi, %r9d
andl $0x7, %r9d
movb (%r9,%rcx), %r9b
xorl %r10d, %r10d
testb %r9b, (%rdi,%r8)
setne %r10b
cmpl %edx, %r10d
je 0x186ce
incl %esi
cmpl %eax, %esi
jl 0x186a1
jmp 0x186d0
movl %esi, %eax
popq %rbx
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/lib/bits.c
// Function: bitClearRange
void bitClearRange(Bits *b, int startIx, int bitCount)
/* Clear a range of bits. */
{
if (bitCount <= 0)
    return;
int endIx = (startIx + bitCount - 1);
int startByte = (startIx>>3);
int endByte = (endIx>>3);
int startBits = (startIx&7);
int endBits = (endIx&7);
int i;

if (startByte == endByte)
    {
    b[startByte] &= ~(leftMask[startBits] & rightMask[endBits]);
    return;
    }
b[startByte] &= ~leftMask[startBits];
for (i = startByte+1; i<endByte; ++i)
    b[i] = 0x00;
b[endByte] &= ~rightMask[endBits];
}

// Assembly:
testl %edx, %edx
jle 0x18757
leal (%rsi,%rdx), %eax
decl %eax
movl %esi, %ecx
sarl $0x3, %ecx
movl %eax, %r8d
sarl $0x3, %r8d
andl $0x7, %esi
andl $0x7, %eax
leaq 0x65496(%rip), %rdx     # 0x7dbae
movb (%rsi,%rdx), %dl
cmpl %r8d, %ecx
jne 0x1872f
leaq 0x6548f(%rip), %rsi     # 0x7dbb6
andb (%rax,%rsi), %dl
movslq %ecx, %rcx
jmp 0x18752
notb %dl
movslq %ecx, %rsi
andb %dl, (%rdi,%rsi)
movslq %r8d, %rcx
incq %rsi
cmpq %rcx, %rsi
jge 0x18748
movb $0x0, (%rdi,%rsi)
jmp 0x1873a
leaq 0x65467(%rip), %rdx     # 0x7dbb6
movb (%rax,%rdx), %dl
notb %dl
andb %dl, (%rdi,%rcx)
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/lib/bits.c
// Function: bitAnd
void bitAnd(Bits *a, Bits *b, int bitCount)
/* And two bitmaps.  Put result in a. */
{
int byteCount = ((bitCount+7)>>3);
while (--byteCount >= 0)
    {
    *a = (*a & *b++);
    a++;
    }
}

// Assembly:
addl $0x7, %edx
sarl $0x3, %edx
xorl %eax, %eax
testl %edx, %edx
jle 0x18771
decl %edx
movb (%rsi,%rax), %cl
andb %cl, (%rdi,%rax)
incq %rax
jmp 0x18760
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/lib/bits.c
// Function: bitAndCount
int bitAndCount(Bits *a, Bits *b, int bitCount)
// Without altering 2 bitmaps, count the AND bits.
{
int byteCount = ((bitCount+7)>>3);
int count = 0;
if (!inittedBitsInByte)
    bitsInByteInit();
while (--byteCount >= 0)
    count += bitsInByte[(*a++ & *b++)];

return count;
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
movl %edx, %ebx
movq %rsi, %r14
movq %rdi, %r15
addl $0x7, %ebx
cmpb $0x0, 0x9c8a7(%rip)     # 0xb5030
jne 0x18790
callq 0x18344
sarl $0x3, %ebx
xorl %ecx, %ecx
leaq 0x9c8a4(%rip), %rdx     # 0xb5040
xorl %eax, %eax
testl %ebx, %ebx
jle 0x187b8
decl %ebx
movzbl (%r15,%rcx), %esi
movzbl (%r14,%rcx), %edi
andl %esi, %edi
addl (%rdx,%rdi,4), %eax
incq %rcx
jmp 0x1879e
popq %rbx
popq %r14
popq %r15
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/lib/bits.c
// Function: bitOr
void bitOr(Bits *a, Bits *b, int bitCount)
/* Or two bitmaps.  Put result in a. */
{
int byteCount = ((bitCount+7)>>3);
while (--byteCount >= 0)
    {
    *a = (*a | *b++);
    a++;
    }
}

// Assembly:
addl $0x7, %edx
sarl $0x3, %edx
xorl %eax, %eax
testl %edx, %edx
jle 0x187d7
decl %edx
movb (%rsi,%rax), %cl
orb %cl, (%rdi,%rax)
incq %rax
jmp 0x187c6
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/lib/bits.c
// Function: bitOrCount
int bitOrCount(Bits *a, Bits *b, int bitCount)
// Without altering 2 bitmaps, count the OR'd bits.
{
int byteCount = ((bitCount+7)>>3);
int count = 0;
if (!inittedBitsInByte)
    bitsInByteInit();
while (--byteCount >= 0)
    count += bitsInByte[(*a++ | *b++)];

return count;
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
movl %edx, %ebx
movq %rsi, %r14
movq %rdi, %r15
addl $0x7, %ebx
cmpb $0x0, 0x9c841(%rip)     # 0xb5030
jne 0x187f6
callq 0x18344
sarl $0x3, %ebx
xorl %ecx, %ecx
leaq 0x9c83e(%rip), %rdx     # 0xb5040
xorl %eax, %eax
testl %ebx, %ebx
jle 0x1881e
decl %ebx
movb (%r14,%rcx), %sil
orb (%r15,%rcx), %sil
movzbl %sil, %esi
addl (%rdx,%rsi,4), %eax
incq %rcx
jmp 0x18804
popq %rbx
popq %r14
popq %r15
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/lib/bits.c
// Function: bitXor
void bitXor(Bits *a, Bits *b, int bitCount)
{
int byteCount = ((bitCount+7)>>3);
while (--byteCount >= 0)
    {
    *a = (*a ^ *b++);
    a++;
    }
}

// Assembly:
addl $0x7, %edx
sarl $0x3, %edx
xorl %eax, %eax
testl %edx, %edx
jle 0x1883d
decl %edx
movb (%rsi,%rax), %cl
xorb %cl, (%rdi,%rax)
incq %rax
jmp 0x1882c
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/lib/bits.c
// Function: bitNot
void bitNot(Bits *a, int bitCount)
/* Flip all bits in a. */
{
int byteCount = ((bitCount+7)>>3);
while (--byteCount >= 0)
    {
    *a = ~*a;
    a++;
    }
}

// Assembly:
addl $0x7, %esi
sarl $0x3, %esi
testl %esi, %esi
jle 0x1889d
decl %esi
notb (%rdi)
incq %rdi
jmp 0x18890
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/lib/bits.c
// Function: bitReverseRange
void bitReverseRange(Bits *bits, int startIx, int bitCount)
// Reverses bits in range (e.g. 110010 becomes 010011)
{
if (bitCount <= 0)
    return;
int ixA = startIx;
int ixB = (startIx + bitCount - 1);
for ( ;ixA < ixB; ixA++, ixB--)
    {
    boolean bitA = bitReadOne(bits, ixA);
    boolean bitB = bitReadOne(bits, ixB);
    if (!bitA && bitB)
        {
        bitSetOne(  bits, ixA);
        bitClearOne(bits, ixB);
        }
    else if (bitA && !bitB)
        {
        bitClearOne(bits, ixA);
        bitSetOne(  bits, ixB);
        }
    }
}

// Assembly:
testl %edx, %edx
jle 0x1891c
pushq %rbx
leal (%rdx,%rsi), %eax
decl %eax
leaq 0x652f7(%rip), %rcx     # 0x7dba6
cmpl %eax, %esi
jge 0x1891b
movl %esi, %edx
sarl $0x3, %edx
movslq %edx, %r9
movb (%rdi,%r9), %r10b
movl %esi, %edx
andl $0x7, %edx
movb (%rdx,%rcx), %r11b
movl %eax, %edx
sarl $0x3, %edx
movslq %edx, %rdx
movl %eax, %r8d
andl $0x7, %r8d
movb (%r8,%rcx), %r8b
movb (%rdi,%rdx), %bl
andb %r8b, %bl
testb %r10b, %r11b
jne 0x188fa
testb %bl, %bl
je 0x188fa
orb %r10b, %r11b
movb %r11b, (%rdi,%r9)
notb %r8b
andb (%rdi,%rdx), %r8b
jmp 0x18911
testb %r10b, %r11b
je 0x18915
testb %bl, %bl
jne 0x18915
notb %r11b
andb %r11b, %r10b
movb %r10b, (%rdi,%r9)
orb (%rdi,%rdx), %r8b
movb %r8b, (%rdi,%rdx)
incl %esi
decl %eax
jmp 0x188af
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/lib/bits.c
// Function: bitPrint
void bitPrint(Bits *a, int startIx, int bitCount, FILE* out)
/* Print part or all of bit map as a string of 0s and 1s.  Mostly useful for
 * debugging */
{
int i;
for (i = startIx; i < bitCount; i++)
    {
    if (bitReadOne(a, i))
        fputc('1', out);
    else
        fputc('0', out);
    }
fputc('\n', out);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %rcx, %rbx
movl %edx, %ebp
movl %esi, %r14d
movq %rdi, %r15
leaq 0x6526c(%rip), %r12     # 0x7dba6
pushq $0x31
popq %r13
cmpl %ebp, %r14d
jge 0x1896f
movl %r14d, %eax
sarl $0x3, %eax
cltq
movl %r14d, %ecx
andl $0x7, %ecx
movb (%rcx,%r12), %cl
andb (%r15,%rax), %cl
cmpb $0x1, %cl
movl %r13d, %edi
sbbl $0x0, %edi
movq %rbx, %rsi
callq 0x6930
incl %r14d
jmp 0x1893e
pushq $0xa
popq %rdi
movq %rbx, %rsi
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
jmp 0x6930
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/lib/bits.c
// Function: bitsOut
void bitsOut(FILE* out, Bits *bits, int startIx, int bitCount, boolean onlyOnes)
// Print part or all of bit map as a string of 0s and 1s.
// If onlyOnes, enclose result in [] and use ' ' instead of '0'.
{
if (onlyOnes)
    fputc('[', out);

int ix = startIx;
for ( ; ix < bitCount; ix++)
    {
    if (bitReadOne(bits, ix))
        fputc('1', out);
    else
        {
        if (onlyOnes)
            fputc(' ', out);
        else
            fputc('0', out);
        }
    }
if (onlyOnes)
    fputc(']', out);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movl %r8d, %ebp
movl %ecx, %r14d
movl %edx, %r15d
movq %rsi, %r12
movq %rdi, %rbx
testl %r8d, %r8d
je 0x189b2
pushq $0x5b
popq %rdi
movq %rbx, %rsi
callq 0x6930
xorl %r13d, %r13d
movl %ebp, 0x4(%rsp)
testl %ebp, %ebp
sete %r13b
shll $0x4, %r13d
orl $0x20, %r13d
leaq 0x651d8(%rip), %rbp     # 0x7dba6
cmpl %r14d, %r15d
jge 0x189fd
movl %r15d, %eax
sarl $0x3, %eax
cltq
movl %r15d, %ecx
andl $0x7, %ecx
movb (%rcx,%rbp), %cl
movl %r13d, %edi
testb %cl, (%r12,%rax)
je 0x189f0
pushq $0x31
popq %rdi
movq %rbx, %rsi
callq 0x6930
incl %r15d
jmp 0x189ce
cmpl $0x0, 0x4(%rsp)
je 0x18a1d
pushq $0x5d
popq %rdi
movq %rbx, %rsi
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
jmp 0x6930
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/lib/bits.c
// Function: bitsIn
Bits *bitsIn(struct lm *lm,char *bitString, int len)
// Returns a bitmap from a string of 1s and 0s.  Any non-zero, non-blank char sets a bit.
// Returned bitmap is the size of len even if that is longer than the string.
// Optionally supply local memory.  Note does NOT handle enclosing []s printed with bitsOut().
{
if (bitString == NULL || len == 0)
    return NULL;

Bits *bits = NULL;
if (lm != NULL)
    bits = lmBitAlloc(lm,len);
else
    bits = bitAlloc(len);

int ix = 0;
for ( ;ix < len && bitString[ix] != '\0'; ix++)
    {
    if (bitString[ix] != '0' && bitString[ix] != ' ')
        bitSetOne(bits, ix);
    }
return bits;
}

// Assembly:
testq %rsi, %rsi
sete %al
testl %edx, %edx
sete %cl
orb %al, %cl
je 0x18a3e
xorl %eax, %eax
retq
pushq %r14
pushq %rbx
pushq %rax
movl %edx, %ebx
movq %rsi, %r14
testq %rdi, %rdi
je 0x18a55
movl %ebx, %esi
callq 0x18402
jmp 0x18a5c
movl %ebx, %edi
callq 0x183ab
xorl %ecx, %ecx
testl %ebx, %ebx
cmovlel %ecx, %ebx
leaq 0x6513c(%rip), %rdx     # 0x7dba6
cmpq %rcx, %rbx
je 0x18a99
movzbl (%r14,%rcx), %esi
cmpl $0x20, %esi
je 0x18a94
cmpl $0x30, %esi
je 0x18a94
testl %esi, %esi
je 0x18a99
movl %ecx, %esi
andl $0x7, %esi
movb (%rsi,%rdx), %sil
movl %ecx, %edi
shrl $0x3, %edi
orb %sil, (%rax,%rdi)
incq %rcx
jmp 0x18a6a
addq $0x8, %rsp
popq %rbx
popq %r14
retq
nopl (%rax)
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/lib/binRange.c
// Function: binFromRange
int binFromRange(int start, int end)
/* return bin that this start-end segment is in */
{
if (end <= BINRANGE_MAXEND_512M)
    return binFromRangeStandard(start, end);
else
    return binFromRangeExtended(start, end);
}

// Assembly:
pushq %rbx
movl %esi, %edx
movl %edi, %esi
leal -0x1(%rdx), %eax
movl %edi, %ebx
sarl $0x11, %ebx
cmpl $0x20000000, %edx       # imm = 0x20000000
jg 0x18b48
sarl $0x11, %eax
xorl %ecx, %ecx
cmpl $0x14, %ecx
je 0x18b62
cmpl %eax, %ebx
je 0x18b7d
sarl $0x3, %ebx
sarl $0x3, %eax
addq $0x4, %rcx
jmp 0x18b33
shrl $0x11, %eax
xorl %ecx, %ecx
cmpl $0x18, %ecx
je 0x18b6b
cmpl %eax, %ebx
je 0x18b89
sarl $0x3, %ebx
shrl $0x3, %eax
addq $0x4, %rcx
jmp 0x18b4d
leaq 0x6518a(%rip), %rdi     # 0x7dcf3
jmp 0x18b72
leaq 0x651b8(%rip), %rdi     # 0x7dd2a
xorl %ebx, %ebx
xorl %eax, %eax
callq 0x223fb
jmp 0x18b9b
leaq 0x651fc(%rip), %rax     # 0x7dd80
addl (%rcx,%rax), %ebx
jmp 0x18b9b
leaq 0x651d0(%rip), %rax     # 0x7dd60
movl (%rcx,%rax), %eax
addl %eax, %ebx
addl $0x1249, %ebx           # imm = 0x1249
movl %ebx, %eax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/lib/binRange.c
// Function: binKeeperNew
struct binKeeper *binKeeperNew(int minPos, int maxPos)
/* Create new binKeeper that can cover range. */
{
int binCount;
struct binKeeper *bk;
if (minPos < 0 || maxPos < 0 || minPos > maxPos)
    errAbort("bad range %d,%d in binKeeperNew", minPos, maxPos);

binCount = binFromRangeBinKeeperExtended(maxPos-1, maxPos) + 1;
AllocVar(bk);
bk->minPos = minPos;
bk->maxPos = maxPos;
bk->binCount = binCount;
AllocArray(bk->binLists, binCount);
return bk;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
movl %esi, %ebx
movl %edi, %ebp
movl %esi, %eax
orl %edi, %eax
setns %al
cmpl %esi, %edi
setle %cl
testb %al, %cl
jne 0x18bcd
leaq 0x65099(%rip), %rdi     # 0x7dc5b
movl %ebp, %esi
movl %ebx, %edx
xorl %eax, %eax
callq 0x223fb
leal -0x1(%rbx), %edi
movl %ebx, %esi
callq 0x18c13
movl %eax, %r14d
leal 0x1(%r14), %r12d
pushq $0x20
popq %rdi
callq 0x28bb0
movq %rax, %r15
movl %ebp, 0x8(%rax)
movl %ebx, 0xc(%rax)
movl %r12d, 0x10(%rax)
movslq %r14d, %rax
leaq 0x8(,%rax,8), %rdi
callq 0x28a1f
movq %rax, 0x18(%r15)
movq %r15, %rax
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/lib/binRange.c
// Function: binFromRangeBinKeeperExtended
static int binFromRangeBinKeeperExtended(int start, int end)
/* This is just like binFromRangeExtended() above, but it doesn't limit
 * the answers to the range from _binOffsetOldToExtended and up.
 *	It simply uses the whole new bin scheme as if it was the only
 *	one.
 */
{
int startBin = start, endBin = end-1, i;
startBin >>= _binFirstShift;
endBin >>= _binFirstShift;
for (i=0; i<ArraySize(binOffsetsExtended); ++i)
    {
    if (startBin == endBin)
	return binOffsetsExtended[i] + startBin;
    startBin >>= _binNextShift;
    endBin >>= _binNextShift;
    }
errAbort("start %d, end %d out of range in findBin (max is 2Gb)", start, end);
return 0;
}

// Assembly:
pushq %rbx
movl %esi, %edx
movl %edi, %esi
leal -0x1(%rdx), %eax
movl %edi, %ebx
sarl $0x11, %ebx
sarl $0x11, %eax
xorl %ecx, %ecx
cmpl $0x18, %ecx
je 0x18c3a
cmpl %eax, %ebx
je 0x18c4c
sarl $0x3, %ebx
sarl $0x3, %eax
addq $0x4, %rcx
jmp 0x18c25
leaq 0x650e9(%rip), %rdi     # 0x7dd2a
xorl %ebx, %ebx
xorl %eax, %eax
callq 0x223fb
jmp 0x18c56
leaq 0x6510d(%rip), %rax     # 0x7dd60
addl (%rcx,%rax), %ebx
movl %ebx, %eax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/lib/binRange.c
// Function: binKeeperFree
void binKeeperFree(struct binKeeper **pBk)
/* Free up a bin keeper. */
{
struct binKeeper *bk = *pBk;
if (bk != NULL)
    {
    int i;
    for (i=0; i<bk->binCount; ++i)
	slFreeList(&bk->binLists[i]);
    freeMem(bk->binLists);
    freez(pBk);
    }
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
movq (%rdi), %r14
testq %r14, %r14
je 0x18ca9
movq %rdi, %rbx
xorl %r15d, %r15d
xorl %r12d, %r12d
movslq 0x10(%r14), %rax
movq 0x18(%r14), %rdi
cmpq %rax, %r12
jge 0x18c91
addq %r15, %rdi
callq 0x1c583
incq %r12
addq $0x8, %r15
jmp 0x18c73
callq 0x28c2d
movq %rbx, %rdi
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
jmp 0x28c3d
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/lib/binRange.c
// Function: binKeeperAdd
void binKeeperAdd(struct binKeeper *bk, int start, int end, void *val)
/* Add item to binKeeper. */ 
{
int bin;
struct binElement *el;
if (start < bk->minPos || end > bk->maxPos || start > end)
    errAbort("(%d %d) out of range (%d %d) in binKeeperAdd", 
    	start, end, bk->minPos, bk->maxPos);
bin = binFromRangeBinKeeperExtended(start, end);
assert(bin < bk->binCount);
AllocVar(el);
el->start = start;
el->end = end;
el->val = val;
slAddHead(&bk->binLists[bin], el);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
movq %rcx, %rbx
movl %edx, %ebp
movl %esi, %r15d
movq %rdi, %r14
movl 0x8(%rdi), %ecx
movl 0xc(%rdi), %r8d
cmpl %esi, %ecx
jg 0x18ce3
cmpl %ebp, %r8d
setge %al
cmpl %ebp, %r15d
setle %dl
testb %al, %dl
jne 0x18cf6
leaq 0x64f91(%rip), %rdi     # 0x7dc7b
movl %r15d, %esi
movl %ebp, %edx
xorl %eax, %eax
callq 0x223fb
movl %r15d, %edi
movl %ebp, %esi
callq 0x18c13
cmpl 0x10(%r14), %eax
jge 0x18d37
movl %eax, %r12d
pushq $0x18
popq %rdi
callq 0x28bb0
movl %r15d, 0x8(%rax)
movl %ebp, 0xc(%rax)
movq %rbx, 0x10(%rax)
movq 0x18(%r14), %rcx
movslq %r12d, %rdx
movq (%rcx,%rdx,8), %rsi
movq %rsi, (%rax)
movq %rax, (%rcx,%rdx,8)
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq
leaq 0x64f6a(%rip), %rdi     # 0x7dca8
leaq 0x64ead(%rip), %rsi     # 0x7dbf2
leaq 0x64f6f(%rip), %rcx     # 0x7dcbb
movl $0xb4, %edx
callq 0x6460
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/lib/binRange.c
// Function: binKeeperFind
struct binElement *binKeeperFind(struct binKeeper *bk, int start, int end)
/* Return a list of all items in binKeeper that intersect range.
 * Free this list with slFreeList. */
{
struct binElement *list = NULL, *newEl, *el;
int startBin, endBin;
int i,j;

if (start < bk->minPos) start = bk->minPos;
if (end > bk->maxPos) end = bk->maxPos;
if (start >= end) return NULL;
startBin = (start>>_binFirstShift);
endBin = ((end-1)>>_binFirstShift);
for (i=0; i<ArraySize(binOffsetsExtended); ++i)
    {
    int offset = binOffsetsExtended[i];
    for (j=startBin+offset; j<=endBin+offset; ++j)
        {
	for (el=bk->binLists[j]; el != NULL; el = el->next)
	    {
	    if (rangeIntersection(el->start, el->end, start, end) > 0)
	        {
		newEl = CloneVar(el);
		slAddHead(&list, newEl);
		}
	    }
	}
    startBin >>= _binNextShift;
    endBin >>= _binNextShift;
    }
return list;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x28, %rsp
movl %edx, %ebx
movl %esi, %ebp
movl 0x8(%rdi), %eax
movq %rdi, 0x20(%rsp)
movl 0xc(%rdi), %ecx
cmpl %esi, %eax
cmovgl %eax, %ebp
cmpl %edx, %ecx
cmovll %ecx, %ebx
cmpl %ebx, %ebp
jge 0x18e36
movl %ebp, %ecx
sarl $0x11, %ecx
leal -0x1(%rbx), %edx
sarl $0x11, %edx
xorl %eax, %eax
xorl %r15d, %r15d
cmpq $0x6, %rax
je 0x18e39
movq %rax, 0x10(%rsp)
leaq 0x64fa8(%rip), %rsi     # 0x7dd60
movl (%rsi,%rax,4), %eax
movq %rcx, 0x18(%rsp)
addl %eax, %ecx
movl %edx, 0xc(%rsp)
addl %edx, %eax
movslq %ecx, %r12
movslq %eax, %r14
cmpq %r14, %r12
jg 0x18e1a
leaq (,%r12,8), %r13
movq 0x20(%rsp), %rax
addq 0x18(%rax), %r13
movq (%r13), %r13
testq %r13, %r13
je 0x18e15
movl 0x8(%r13), %edi
movl 0xc(%r13), %esi
movl %ebp, %edx
movl %ebx, %ecx
callq 0x1f506
testl %eax, %eax
jle 0x18de4
movq %r13, %rdi
pushq $0x18
popq %rsi
callq 0x1c27c
movq %r15, (%rax)
movq %rax, %r15
jmp 0x18de4
incq %r12
jmp 0x18dce
movq 0x18(%rsp), %rcx
sarl $0x3, %ecx
movl 0xc(%rsp), %edx
sarl $0x3, %edx
movq 0x10(%rsp), %rax
incq %rax
jmp 0x18da2
xorl %r15d, %r15d
movq %r15, %rax
addq $0x28, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/lib/binRange.c
// Function: binKeeperAnyOverlap
boolean binKeeperAnyOverlap(struct binKeeper *bk, int start, int end)
/* Return TRUE if start/end overlaps with any items in binKeeper. */
{
struct binElement *el;
int startBin, endBin;
int i,j;

if (start < bk->minPos) start = bk->minPos;
if (end > bk->maxPos) end = bk->maxPos;
if (start >= end) return FALSE;
startBin = (start>>_binFirstShift);
endBin = ((end-1)>>_binFirstShift);
for (i=0; i<ArraySize(binOffsetsExtended); ++i)
    {
    int offset = binOffsetsExtended[i];
    for (j=startBin+offset; j<=endBin+offset; ++j)
        {
	for (el=bk->binLists[j]; el != NULL; el = el->next)
	    {
	    if (rangeIntersection(el->start, el->end, start, end) > 0)
	        {
		return TRUE;
		}
	    }
	}
    startBin >>= _binNextShift;
    endBin >>= _binNextShift;
    }
return FALSE;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x28, %rsp
movl %edx, %ebx
movl %esi, %ebp
movl 0x8(%rdi), %eax
movl 0xc(%rdi), %ecx
cmpl %esi, %eax
cmovgl %eax, %ebp
cmpl %edx, %ecx
cmovll %ecx, %ebx
xorl %r15d, %r15d
cmpl %ebx, %ebp
jge 0x18f1f
movq %rdi, %r14
movl %ebp, %ecx
sarl $0x11, %ecx
leal -0x1(%rbx), %edx
sarl $0x11, %edx
xorl %r15d, %r15d
leaq 0x64ed0(%rip), %rax     # 0x7dd60
xorl %esi, %esi
cmpq $0x6, %rsi
je 0x18f1f
movq %rsi, 0x10(%rsp)
movl (%rax,%rsi,4), %eax
movq %rcx, 0x18(%rsp)
addl %eax, %ecx
movl %edx, 0xc(%rsp)
addl %edx, %eax
movslq %ecx, %r12
cltq
movq %rax, 0x20(%rsp)
cmpq %rax, %r12
jg 0x18ef6
leaq (,%r12,8), %r13
addq 0x18(%r14), %r13
movq (%r13), %r13
testq %r13, %r13
je 0x18eec
movl 0x8(%r13), %edi
movl 0xc(%r13), %esi
movl %ebp, %edx
movl %ebx, %ecx
callq 0x1f506
testl %eax, %eax
jle 0x18ecc
jmp 0x18f19
incq %r12
movq 0x20(%rsp), %rax
jmp 0x18ebb
movq 0x18(%rsp), %rcx
sarl $0x3, %ecx
movl 0xc(%rsp), %edx
sarl $0x3, %edx
movq 0x10(%rsp), %rsi
incq %rsi
leaq 0x64e4c(%rip), %rax     # 0x7dd60
jmp 0x18e92
pushq $0x1
popq %rax
movl %eax, %r15d
movl %r15d, %eax
addq $0x28, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/lib/binRange.c
// Function: binKeeperReplaceVal
void binKeeperReplaceVal(struct binKeeper *bk, int start, int end,
	void *oldVal, void *newVal)
/* Replace occurences of old val in range from start->end with newVal */
{
struct binElement *el;
int startBin, endBin;
int i,j;

if (start < bk->minPos) start = bk->minPos;
if (end > bk->maxPos) end = bk->maxPos;
if (start >= end) return;
startBin = (start>>_binFirstShift);
endBin = ((end-1)>>_binFirstShift);
for (i=0; i<ArraySize(binOffsetsExtended); ++i)
    {
    int offset = binOffsetsExtended[i];
    for (j=startBin+offset; j<=endBin+offset; ++j)
        {
	for (el=bk->binLists[j]; el != NULL; el = el->next)
	    {
	    if (rangeIntersection(el->start, el->end, start, end) > 0)
	        {
		if (el->val == oldVal)
		    {
		    el->val = newVal;
		    }
		}
	    }
	}
    startBin >>= _binNextShift;
    endBin >>= _binNextShift;
    }
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x28, %rsp
movq %rcx, %r14
movl %edx, %r15d
movl %esi, %ebp
movl 0x8(%rdi), %eax
movq %rdi, 0x18(%rsp)
movl 0xc(%rdi), %ecx
cmpl %esi, %eax
cmovgl %eax, %ebp
cmpl %edx, %ecx
cmovll %ecx, %r15d
cmpl %r15d, %ebp
jge 0x1900f
movq %r8, %rbx
movl %ebp, %ecx
sarl $0x11, %ecx
leal -0x1(%r15), %edx
sarl $0x11, %edx
xorl %eax, %eax
cmpq $0x6, %rax
je 0x1900f
movq %rax, 0x8(%rsp)
leaq 0x64dd3(%rip), %rsi     # 0x7dd60
movl (%rsi,%rax,4), %eax
movq %rcx, 0x10(%rsp)
addl %eax, %ecx
movl %edx, 0x4(%rsp)
addl %edx, %eax
movslq %ecx, %r13
cltq
movq %rax, 0x20(%rsp)
cmpq 0x20(%rsp), %r13
jg 0x18ff3
leaq (,%r13,8), %r12
movq 0x18(%rsp), %rax
addq 0x18(%rax), %r12
movq (%r12), %r12
testq %r12, %r12
je 0x18fee
movl 0x8(%r12), %edi
movl 0xc(%r12), %esi
movl %ebp, %edx
movl %r15d, %ecx
callq 0x1f506
testl %eax, %eax
jle 0x18fbf
cmpq %r14, 0x10(%r12)
jne 0x18fbf
movq %rbx, 0x10(%r12)
jmp 0x18fbf
incq %r13
jmp 0x18fa7
movq 0x10(%rsp), %rcx
sarl $0x3, %ecx
movl 0x4(%rsp), %edx
sarl $0x3, %edx
movq 0x8(%rsp), %rax
incq %rax
jmp 0x18f77
addq $0x28, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/lib/binRange.c
// Function: binKeeperFindLowest
struct binElement *binKeeperFindLowest(struct binKeeper *bk, int start, int end)
/* Find the lowest overlapping range. Quick even if search range large */
{
struct binElement *first = NULL, *el;
int startBin = (start>>_binFirstShift), endBin = ((end-1)>>_binFirstShift);
int i,j;

/* Search the possible range of bins at each level, looking for lowest.  Once
 * an overlaping range is found at a level, continue with next level, however
 * must search an entire bin as they are not ordered. */
for (i=0; i<ArraySize(binOffsetsExtended); ++i)
    {
    int offset = binOffsetsExtended[i];
    boolean foundOne = FALSE;
    for (j=startBin+offset; (j<=endBin+offset) && (!foundOne); ++j)
        {
	for (el=bk->binLists[j]; el != NULL; el = el->next)
	    {
            if ((rangeIntersection(el->start, el->end, start, end) > 0)
                && ((first == NULL) || (el->start < first->start)
                    || ((el->start == first->start)
                        && (el->end < first->end))))
                {
                first = el;
                foundOne = TRUE;
		}
	    }
	}
    startBin >>= _binNextShift;
    endBin >>= _binNextShift;
    }
return first;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x28, %rsp
movl %edx, %ebx
movl %esi, %ebp
movq %rdi, 0x18(%rsp)
movl %esi, %ecx
sarl $0x11, %ecx
leal -0x1(%rbx), %edx
sarl $0x11, %edx
xorl %eax, %eax
xorl %r13d, %r13d
cmpq $0x6, %rax
je 0x1912f
movq %rax, 0x8(%rsp)
leaq 0x64cd0(%rip), %rsi     # 0x7dd60
movl (%rsi,%rax,4), %eax
movq %rcx, 0x10(%rsp)
addl %eax, %ecx
movl %edx, 0x4(%rsp)
addl %edx, %eax
movslq %ecx, %r12
cltq
movq %rax, 0x20(%rsp)
xorl %r14d, %r14d
cmpq 0x20(%rsp), %r12
jg 0x19113
testl %r14d, %r14d
jne 0x19113
leaq (,%r12,8), %r15
movq 0x18(%rsp), %rax
addq 0x18(%rax), %r15
xorl %r14d, %r14d
movq (%r15), %r15
testq %r15, %r15
je 0x1910e
movl 0x8(%r15), %edi
movl 0xc(%r15), %esi
movl %ebp, %edx
movl %ebx, %ecx
callq 0x1f506
testl %eax, %eax
jle 0x190cd
testq %r13, %r13
je 0x19105
movl 0x8(%r13), %eax
cmpl %eax, 0x8(%r15)
jl 0x19105
jne 0x190cd
movl 0xc(%r15), %eax
cmpl 0xc(%r13), %eax
jge 0x190cd
movq %r15, %r13
pushq $0x1
popq %r14
jmp 0x190cd
incq %r12
jmp 0x190ad
movq 0x10(%rsp), %rcx
sarl $0x3, %ecx
movl 0x4(%rsp), %edx
sarl $0x3, %edx
movq 0x8(%rsp), %rax
incq %rax
jmp 0x1907a
movq %r13, %rax
addq $0x28, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/lib/binRange.c
// Function: binKeeperRemove
void binKeeperRemove(struct binKeeper *bk, int start, int end, void *val)
/* Remove item from binKeeper. */ 
{
int bin = binFromRangeBinKeeperExtended(start, end);
struct binElement **pList = &bk->binLists[bin], *newList = NULL, *el, *next;
for (el = *pList; el != NULL; el = next)
    {
    next = el->next;
    if (el->val == val && el->start == start && el->end == end)
        {
	freeMem(el);
	}
    else
        {
	slAddHead(&newList, el);
	}
    }
slReverse(&newList);
*pList = newList;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x18, %rsp
movq %rcx, %rbx
movl %edx, %ebp
movl %esi, %r14d
movq %rdi, %r15
movl %esi, %edi
movl %edx, %esi
callq 0x18c13
movq 0x18(%r15), %rcx
andq $0x0, 0x8(%rsp)
movslq %eax, %r12
movq %rcx, 0x10(%rsp)
movq (%rcx,%r12,8), %r13
xorl %edi, %edi
movq %rdi, %r15
movq %r13, %rdi
testq %r13, %r13
je 0x191ab
movq (%rdi), %r13
cmpq %rbx, 0x10(%rdi)
jne 0x191a1
cmpl %r14d, 0x8(%rdi)
jne 0x191a1
cmpl %ebp, 0xc(%rdi)
jne 0x191a1
callq 0x28c2d
jmp 0x1917e
movq %r15, (%rdi)
movq %rdi, 0x8(%rsp)
jmp 0x1917b
leaq 0x8(%rsp), %rbx
movq %rbx, %rdi
callq 0x1c567
movq (%rbx), %rax
movq 0x10(%rsp), %rcx
movq %rax, (%rcx,%r12,8)
addq $0x18, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/lib/binRange.c
// Function: binKeeperNext
struct binElement* binKeeperNext(struct binKeeperCookie *cookie)
/* Return the next entry in the binKeeper table.  */
{
/* if we don't have a next, move down bin list until we find one */
while ((cookie->nextBel == NULL)
       && (++cookie->blIdx < cookie->bk->binCount))
    cookie->nextBel = cookie->bk->binLists[cookie->blIdx];
if (cookie->blIdx >= cookie->bk->binCount)
    return NULL;  /* no more */
else
    {
    struct binElement* bel = cookie->nextBel;
    cookie->nextBel = cookie->nextBel->next;
    return bel;
    }
}

// Assembly:
movq 0x10(%rdi), %rax
movl 0x8(%rdi), %ecx
movq (%rdi), %rdx
leal 0x1(%rcx), %esi
movslq %esi, %rsi
testq %rax, %rax
jne 0x19222
leal 0x1(%rcx), %r9d
movl %r9d, 0x8(%rdi)
movl 0x10(%rdx), %r8d
cmpl %r8d, %r9d
jge 0x19228
movq 0x18(%rdx), %rax
movq (%rax,%rsi,8), %rax
movq %rax, 0x10(%rdi)
incq %rsi
incl %ecx
jmp 0x191f9
movl 0x10(%rdx), %r8d
jmp 0x1922b
movl %r9d, %ecx
cmpl %r8d, %ecx
jge 0x19238
movq (%rax), %rcx
movq %rcx, 0x10(%rdi)
retq
xorl %eax, %eax
retq
nop
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/lib/blastOut.c
// Function: bundleIntoTargets
static struct targetHits *bundleIntoTargets(struct axtBundle *abList)
/* BLAST typically outputs everything on the same query and target
 * in one clump.  This routine rearranges axts in abList to do this. */
{
struct targetHits *targetList = NULL, *target;
struct hash *targetHash = newHash(10);
struct axtBundle *ab;
struct axtRef *ref;

/* Build up a list of targets in database hit by query sorted by
 * score of hits. */
for (ab = abList; ab != NULL; ab = ab->next)
    {
    struct axt *axt;
    for (axt = ab->axtList; axt != NULL; axt = axt->next)
	{
	target = hashFindVal(targetHash, axt->tName);
	if (target == NULL)
	    {
	    AllocVar(target);
	    slAddHead(&targetList, target);
	    hashAdd(targetHash, axt->tName, target);
	    target->name = cloneString(axt->tName);
	    target->size = ab->tSize;
	    }
	if (axt->score > target->score)
	    target->score = axt->score;
	AllocVar(ref);
	ref->axt = axt;
	slAddHead(&target->axtList, ref);
	}
    }
slSort(&targetList, targetHitsCmpScore);
for (target = targetList; target != NULL; target = target->next)
    slSort(&target->axtList, axtRefCmpScore);

hashFree(&targetHash);
return targetList;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x18, %rsp
movq %rdi, %rbx
andq $0x0, 0x8(%rsp)
pushq $0xa
popq %rdi
pushq $0x1
popq %rsi
callq 0x245c9
movq %rax, %r14
movq %rax, 0x10(%rsp)
xorl %ebp, %ebp
pushq $0x10
popq %r12
testq %rbx, %rbx
je 0x1a6f3
leaq 0x8(%rbx), %r15
movq (%r15), %r15
testq %r15, %r15
je 0x1a6eb
movq 0x20(%r15), %rsi
movq %r14, %rdi
callq 0x244c6
testq %rax, %rax
je 0x1a68b
movq %rax, %r13
jmp 0x1a6c4
pushq $0x28
popq %rdi
callq 0x28bb0
movq %rax, %r13
movq %rbp, (%rax)
movq %rax, 0x8(%rsp)
movq 0x20(%r15), %rsi
movq %r14, %rdi
movq %rax, %rdx
callq 0x242d0
movq 0x20(%r15), %rdi
callq 0x1c306
movq %rax, 0x8(%r13)
movl 0x10(%rbx), %eax
movl %eax, 0x10(%r13)
movq %r13, %rbp
movl 0x34(%r15), %eax
cmpl 0x20(%r13), %eax
jle 0x1a6d2
movl %eax, 0x20(%r13)
movq %r12, %rdi
callq 0x28bb0
movq %r15, 0x8(%rax)
movq 0x18(%r13), %rcx
movq %rcx, (%rax)
movq %rax, 0x18(%r13)
jmp 0x1a66d
movq (%rbx), %rbx
jmp 0x1a660
leaq 0x422(%rip), %rsi       # 0x1ab1c
leaq 0x8(%rsp), %rbx
movq %rbx, %rdi
callq 0x1c5ab
leaq 0x41b(%rip), %r14       # 0x1ab29
movq (%rbx), %rbx
testq %rbx, %rbx
je 0x1a724
leaq 0x18(%rbx), %rdi
movq %r14, %rsi
callq 0x1c5ab
jmp 0x1a70e
leaq 0x10(%rsp), %rdi
callq 0x2494c
movq 0x8(%rsp), %rax
addq $0x18, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/lib/blastOut.c
// Function: countMatches
static int countMatches(char *a, char *b, int size)
/* Count number of characters that match between a and b. */
{
int count = 0;
int i;
for (i=0; i<size; ++i)
    if (toupper(a[i]) == toupper(b[i]))
        ++count;
return count;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
movl %edx, %ebx
movq %rsi, %r14
movq %rdi, %r15
xorl %r12d, %r12d
testl %edx, %edx
cmovlel %r12d, %ebx
xorl %ebp, %ebp
cmpq %r12, %rbx
je 0x1a7ad
callq 0x6100
movq (%rax), %rax
movsbq (%r15,%r12), %rcx
movl (%rax,%rcx,4), %ecx
movsbq (%r14,%r12), %rdx
xorl %esi, %esi
cmpl (%rax,%rdx,4), %ecx
sete %sil
addl %esi, %ebp
incq %r12
jmp 0x1a783
movl %ebp, %eax
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/lib/blastOut.c
// Function: countPositives
static int countPositives(char *a, char *b, int size)
/* Count positive (not necessarily identical) protein matches. */
{
int count = 0;
int i;
struct axtScoreScheme *ss = axtScoreSchemeProteinDefault();
for (i=0; i<size; ++i)
    {
    if (ss->matrix[(int)a[i]][(int)b[i]] > 0)
        ++count;
    }
return count;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
movl %edx, %ebx
movq %rsi, %r14
movq %rdi, %r15
xorl %r12d, %r12d
xorl %eax, %eax
callq 0x176c4
addq $0x8, %rax
testl %ebx, %ebx
cmovlel %r12d, %ebx
xorl %ecx, %ecx
cmpq %r12, %rbx
je 0x1a805
movsbq (%r15,%r12), %rdx
movsbq (%r14,%r12), %rsi
shlq $0xa, %rdx
addq %rax, %rdx
xorl %edi, %edi
cmpl $0x0, (%rdx,%rsi,4)
setg %dil
addl %edi, %ecx
incq %r12
jmp 0x1a7de
movl %ecx, %eax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/lib/blastOut.c
// Function: targetHitsFreeList
static void targetHitsFreeList(struct targetHits **pList)
/* Free a list of dynamically allocated targetHits's */
{
struct targetHits *el, *next;

for (el = *pList; el != NULL; el = next)
    {
    next = el->next;
    targetHitsFree(&el);
    }
*pList = NULL;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
movq %rdi, %rbx
movq (%rdi), %r15
movq %rsp, %r14
movq %r15, (%rsp)
testq %r15, %r15
je 0x1ab0c
movq (%r15), %r12
movq 0x8(%r15), %rdi
callq 0x28c2d
addq $0x18, %r15
movq %r15, %rdi
callq 0x1c583
movq %r14, %rdi
callq 0x28c3d
movq %r12, %r15
jmp 0x1aade
andq $0x0, (%rbx)
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/lib/blastOut.c
// Function: ncbiPrintE
static void ncbiPrintE(FILE *f, double e)
/* Print a small number NCBI style. */
{
if (e <= 0.0)
    fprintf(f, "0.0");
else if (e <= 1.0e-100)
    {
    char buf[256], *s;
    safef(buf, sizeof(buf), "%e", e);
    s = strchr(buf, 'e');
    if (s == NULL)
	fprintf(f, "0.0");
    else
        fprintf(f, "%s", s);
    }
else
    fprintf(f, "%1.0e", e);
}

// Assembly:
pushq %r14
pushq %rbx
subq $0x108, %rsp            # imm = 0x108
movq %rdi, %rbx
xorpd %xmm1, %xmm1
ucomisd %xmm0, %xmm1
jae 0x1aba2
movsd 0x6325f(%rip), %xmm1    # 0x7dde0
ucomisd %xmm0, %xmm1
jae 0x1abc1
leaq 0x63ed1(%rip), %rsi     # 0x7ea5f
movq %rbx, %rdi
movb $0x1, %al
addq $0x108, %rsp            # imm = 0x108
popq %rbx
popq %r14
jmp 0x6a90
leaq 0x63eaf(%rip), %rdi     # 0x7ea58
pushq $0x3
popq %rsi
pushq $0x1
popq %rdx
movq %rbx, %rcx
addq $0x108, %rsp            # imm = 0x108
popq %rbx
popq %r14
jmp 0x6e70
leaq 0x63e94(%rip), %rdx     # 0x7ea5c
movq %rsp, %r14
movq %r14, %rdi
movl $0x100, %esi            # imm = 0x100
movb $0x1, %al
callq 0x1fab2
pushq $0x65
popq %rsi
movq %r14, %rdi
callq 0x6270
testq %rax, %rax
je 0x1abf7
movq %rax, %rdi
movq %rbx, %rsi
callq 0x6810
jmp 0x1ac0c
leaq 0x63e5a(%rip), %rdi     # 0x7ea58
pushq $0x3
popq %rsi
pushq $0x1
popq %rdx
movq %rbx, %rcx
callq 0x6e70
addq $0x108, %rsp            # imm = 0x108
popq %rbx
popq %r14
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/lib/blastOut.c
// Function: countGaps
static int countGaps(char *a, char *b, int size)
/* Count number of inserts in either strand. */
{
int count = 0;
int i;
for (i=0; i<size; ++i)
   {
   if (a[i] == '-')
       ++count;
   if (b[i] == '-')
       ++count;
   }
return count;
}

// Assembly:
xorl %ecx, %ecx
testl %edx, %edx
cmovlel %ecx, %edx
xorl %eax, %eax
cmpq %rcx, %rdx
je 0x1ac46
xorl %r8d, %r8d
cmpb $0x2d, (%rdi,%rcx)
sete %r8b
addl %r8d, %eax
xorl %r8d, %r8d
cmpb $0x2d, (%rsi,%rcx)
sete %r8b
addl %r8d, %eax
incq %rcx
jmp 0x1ac20
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/lib/blastOut.c
// Function: printAxtTargetBlastTab
static void printAxtTargetBlastTab(FILE *f, struct axt *axt, int targetSize)
/* Print out target in tabular blast-oriented format. */
{
int s = axt->tStart, e = axt->tEnd;
if (axt->tStrand == '-')
    reverseIntRange(&s, &e, targetSize);
if (axt->tStrand == axt->qStrand)
    {
    fprintf(f, "%d\t", s+1);
    fprintf(f, "%d\t", e);
    }
else
    {
    fprintf(f, "%d\t", e);
    fprintf(f, "%d\t", s+1);
    }
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rsi, %r14
movq %rdi, %rbx
movl 0x28(%rsi), %eax
movl %eax, 0x4(%rsp)
movl 0x2c(%rsi), %eax
movl %eax, (%rsp)
movb 0x30(%rsi), %al
cmpb $0x2d, %al
jne 0x1ac76
leaq 0x4(%rsp), %rdi
movq %rsp, %rsi
callq 0x20d61
movb 0x30(%r14), %al
cmpb 0x18(%r14), %al
jne 0x1ac98
movl 0x4(%rsp), %edx
incl %edx
leaq 0x625f5(%rip), %rsi     # 0x7d27e
movq %rbx, %rdi
xorl %eax, %eax
callq 0x6a90
movl (%rsp), %edx
jmp 0x1acb2
movl (%rsp), %edx
leaq 0x625dc(%rip), %rsi     # 0x7d27e
movq %rbx, %rdi
xorl %eax, %eax
callq 0x6a90
movl 0x4(%rsp), %edx
incl %edx
leaq 0x625c5(%rip), %rsi     # 0x7d27e
movq %rbx, %rdi
xorl %eax, %eax
callq 0x6a90
addq $0x8, %rsp
popq %rbx
popq %r14
retq
nop
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/lib/chain.c
// Function: chainFree
void chainFree(struct chain **pChain)
/* Free up a chain. */
{
struct chain *chain = *pChain;
if (chain != NULL)
    {
    slFreeList(&chain->blockList);
    freeMem(chain->qName);
    freeMem(chain->tName);
    freez(pChain);
    }
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq (%rdi), %r14
testq %r14, %r14
je 0x1ad05
movq %rdi, %rbx
leaq 0x8(%r14), %rdi
callq 0x1c583
movq 0x30(%r14), %rdi
callq 0x28c2d
movq 0x18(%r14), %rdi
callq 0x28c2d
movq %rbx, %rdi
addq $0x8, %rsp
popq %rbx
popq %r14
jmp 0x28c3d
addq $0x8, %rsp
popq %rbx
popq %r14
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/lib/chain.c
// Function: chainFreeList
void chainFreeList(struct chain **pList)
/* Free a list of dynamically allocated chain's */
{
struct chain *el, *next;

for (el = *pList; el != NULL; el = next)
    {
    next = el->next;
    chainFree(&el);
    }
*pList = NULL;
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
subq $0x10, %rsp
movq %rdi, %rbx
movq (%rdi), %r15
leaq 0x8(%rsp), %r14
movq %r15, 0x8(%rsp)
testq %r15, %r15
je 0x1ad38
movq (%r15), %r15
movq %r14, %rdi
callq 0x1accc
jmp 0x1ad21
andq $0x0, (%rbx)
addq $0x10, %rsp
popq %rbx
popq %r14
popq %r15
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/lib/chain.c
// Function: cBlocksAddOffset
void cBlocksAddOffset(struct cBlock *blockList, int qOff, int tOff)
/* Add offsets to block list. */
{
struct cBlock *block;
for (block = blockList; block != NULL; block = block->next)
    {
    block->tStart += tOff;
    block->tEnd += tOff;
    block->qStart += qOff;
    block->qEnd += qOff;
    }
}

// Assembly:
movd %esi, %xmm0
movd %edx, %xmm1
punpckldq %xmm0, %xmm1    # xmm1 = xmm1[0],xmm0[0],xmm1[1],xmm0[1]
pshufd $0x50, %xmm1, %xmm0     # xmm0 = xmm1[0,0,1,1]
testq %rdi, %rdi
je 0x1adbd
movdqu 0x8(%rdi), %xmm1
paddd %xmm0, %xmm1
movdqu %xmm1, 0x8(%rdi)
movq (%rdi), %rdi
jmp 0x1ada5
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/lib/chain.c
// Function: cBlocksFromAliSym
struct cBlock *cBlocksFromAliSym(int symCount, char *qSym, char *tSym, 
        int qPos, int tPos)
/* Convert alignment from alignment symbol (bases and dashes) format 
 * to a list of chain blocks.  The qPos and tPos correspond to the start
 * in the query and target sequences of the first letter in  qSym and tSym. */
{
struct cBlock *blockList = NULL, *block = NULL;
int i;
for (i=0; i<symCount; ++i)
    {
    if (qSym[i] == '-')
        {
        block = NULL;
        ++tPos;
        }
    else if (tSym[i] == '-')
        {
        block = NULL;
        ++qPos;
        }
    else
        {
        if (block == NULL)
            {
            AllocVar(block);
            slAddHead(&blockList, block);
            block->qStart = qPos;
            block->tStart = tPos;
            }
        block->qEnd = ++qPos;
        block->tEnd = ++tPos;
        }
    }
slReverse(&blockList);
return blockList;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x18, %rsp
movl %r8d, %ebx
movl %ecx, %ebp
movq %rdx, %r14
movl %edi, %r15d
andq $0x0, 0x8(%rsp)
xorl %ecx, %ecx
testl %edi, %edi
cmovlel %ecx, %r15d
movq %rsi, %r12
xorl %r13d, %r13d
xorl %eax, %eax
cmpq %r13, %r15
je 0x1ae41
cmpb $0x2d, (%r12,%r13)
jne 0x1adfd
incl %ebx
jmp 0x1ae06
cmpb $0x2d, (%r14,%r13)
jne 0x1ae0a
incl %ebp
xorl %eax, %eax
jmp 0x1ae3c
testq %rax, %rax
jne 0x1ae32
pushq $0x28
popq %rdi
movq %rcx, 0x10(%rsp)
callq 0x28bb0
movq 0x10(%rsp), %rcx
movq %rcx, (%rax)
movq %rax, 0x8(%rsp)
movl %ebp, 0x10(%rax)
movl %ebx, 0x8(%rax)
movq %rax, %rcx
incl %ebp
movl %ebp, 0x14(%rax)
incl %ebx
movl %ebx, 0xc(%rax)
incq %r13
jmp 0x1aded
leaq 0x8(%rsp), %rbx
movq %rbx, %rdi
callq 0x1c567
movq (%rbx), %rax
addq $0x18, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/lib/chain.c
// Function: chainCmpScore
int chainCmpScore(const void *va, const void *vb)
/* Compare to sort based on total score. */
{
const struct chain *a = *((struct chain **)va);
const struct chain *b = *((struct chain **)vb);
double diff = b->score - a->score;
if (diff < 0.0) return -1;
else if (diff > 0.0) return 1;
else return 0;
}

// Assembly:
movq (%rdi), %rax
movq (%rsi), %rcx
movsd 0x10(%rcx), %xmm0
subsd 0x10(%rax), %xmm0
xorpd %xmm1, %xmm1
xorl %ecx, %ecx
ucomisd %xmm1, %xmm0
seta %cl
ucomisd %xmm0, %xmm1
pushq $-0x1
popq %rax
cmovbel %ecx, %eax
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/lib/chain.c
// Function: chainCmpTarget
int chainCmpTarget(const void *va, const void *vb)
/* Compare to sort based on target position. */
{
const struct chain *a = *((struct chain **)va);
const struct chain *b = *((struct chain **)vb);
int dif = strcmp(a->tName, b->tName);
if (dif == 0)
    dif = a->tStart - b->tStart;
return dif;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq (%rdi), %r14
movq (%rsi), %rbx
movq 0x18(%r14), %rdi
movq 0x18(%rbx), %rsi
callq 0x6a50
testl %eax, %eax
jne 0x1aed2
movl 0x24(%r14), %eax
subl 0x24(%rbx), %eax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/lib/chain.c
// Function: chainCmpQuery
int chainCmpQuery(const void *va, const void *vb)
/* Compare to sort based on query chrom and target position. */
{
const struct chain *a = *((struct chain **)va);
const struct chain *b = *((struct chain **)vb);
int dif;                                                                        

dif = strcmp(a->qName, b->qName);                                               
if (dif == 0)                                                                   
    dif = a->qStart - b->qStart;                                                
return dif;                       
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq (%rdi), %r14
movq (%rsi), %rbx
movq 0x30(%r14), %rdi
movq 0x30(%rbx), %rsi
callq 0x6a50
testl %eax, %eax
jne 0x1aefc
movl 0x40(%r14), %eax
subl 0x40(%rbx), %eax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/lib/chain.c
// Function: chainWriteHead
void chainWriteHead(struct chain *chain, FILE *f)
/* Write chain before block/insert list. */
{
if (chain->id == 0)
    chainIdNext(chain);
fprintf(f, "chain %1.0f %s %d + %d %d %s %d %c %d %d %d\n", chain->score,
    chain->tName, chain->tSize, chain->tStart, chain->tEnd,
    chain->qName, chain->qSize, chain->qStrand, chain->qStart, chain->qEnd,
    chain->id);
}

// Assembly:
movq %rsi, %rax
movq %rdi, %r10
movl 0x48(%rdi), %r11d
testl %r11d, %r11d
jne 0x1af4d
movl 0x996cd(%rip), %r11d    # 0xb460c
leal 0x1(%r11), %ecx
movl %ecx, 0x996c3(%rip)     # 0xb460c
movl %r11d, 0x48(%r10)
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
movsd 0x10(%r10), %xmm0
movq 0x18(%r10), %rdx
movl 0x20(%r10), %ecx
movl 0x24(%r10), %r8d
movl 0x28(%r10), %r9d
movl 0x38(%r10), %ebx
movsbl 0x3c(%r10), %r14d
movl 0x40(%r10), %r15d
movl 0x44(%r10), %r12d
leaq 0x63bd2(%rip), %rsi     # 0x7eb55
movq %rax, %rdi
movb $0x1, %al
pushq %r11
pushq %r12
pushq %r15
pushq %r14
pushq %rbx
pushq 0x30(%r10)
callq 0x6a90
addq $0x38, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/lib/chain.c
// Function: chainWrite
void chainWrite(struct chain *chain, FILE *f)
/* Write out chain to file in usual format*/
{
struct cBlock *b, *nextB;

chainWriteHead(chain, f);
for (b = chain->blockList; b != NULL; b = nextB)
    {
    nextB = b->next;
    fprintf(f, "%d", b->qEnd - b->qStart);
    if (nextB != NULL)
	fprintf(f, "\t%d\t%d", 
		nextB->tStart - b->tEnd, nextB->qStart - b->qEnd);
    fputc('\n', f);
    }
fputc('\n', f);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %rsi, %rbx
movq %rdi, %r14
callq 0x1af29
movq 0x8(%r14), %r13
leaq 0x63bbf(%rip), %r14     # 0x7eb86
pushq $0xa
popq %rbp
leaq 0x63bb1(%rip), %r15     # 0x7eb82
testq %r13, %r13
je 0x1b022
movq (%r13), %r12
movl 0x14(%r13), %edx
subl 0x10(%r13), %edx
movq %rbx, %rdi
movq %r14, %rsi
xorl %eax, %eax
callq 0x6a90
testq %r12, %r12
je 0x1b013
movl 0x8(%r12), %edx
movl 0x10(%r12), %ecx
subl 0xc(%r13), %edx
subl 0x14(%r13), %ecx
movq %rbx, %rdi
movq %r15, %rsi
xorl %eax, %eax
callq 0x6a90
movl %ebp, %edi
movq %rbx, %rsi
callq 0x6930
movq %r12, %r13
jmp 0x1afd1
pushq $0xa
popq %rdi
movq %rbx, %rsi
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
jmp 0x6930
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/lib/chain.c
// Function: chainWriteLong
void chainWriteLong(struct chain *chain, FILE *f)
/* Write out chain to file in longer format*/
{
struct cBlock *b, *nextB;

chainWriteHead(chain, f);
for (b = chain->blockList; b != NULL; b = nextB)
    {
    nextB = b->next;
    fprintf(f, "%d\t%d\t", b->tStart, b->qStart);
    fprintf(f, "%d", b->qEnd - b->qStart);
    if (nextB != NULL)
	fprintf(f, "\t%d\t%d", 
		nextB->tStart - b->tEnd, nextB->qStart - b->qEnd);
    fputc('\n', f);
    }
fputc('\n', f);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %rsi, %rbx
movq %rdi, %r14
callq 0x1af29
movq 0x8(%r14), %r13
leaq 0x621f8(%rip), %r14     # 0x7d27b
leaq 0x63afc(%rip), %r15     # 0x7eb86
pushq $0xa
popq %rbp
testq %r13, %r13
je 0x1b0f7
movq (%r13), %r12
movl 0x8(%r13), %edx
movl 0x10(%r13), %ecx
movq %rbx, %rdi
movq %r14, %rsi
xorl %eax, %eax
callq 0x6a90
movl 0x14(%r13), %edx
subl 0x10(%r13), %edx
movq %rbx, %rdi
movq %r15, %rsi
xorl %eax, %eax
callq 0x6a90
testq %r12, %r12
je 0x1b0e8
movl 0x8(%r12), %edx
movl 0x10(%r12), %ecx
subl 0xc(%r13), %edx
subl 0x14(%r13), %ecx
movq %rbx, %rdi
leaq 0x63aa1(%rip), %rsi     # 0x7eb82
xorl %eax, %eax
callq 0x6a90
movl %ebp, %edi
movq %rbx, %rsi
callq 0x6930
movq %r12, %r13
jmp 0x1b08d
pushq $0xa
popq %rdi
movq %rbx, %rsi
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
jmp 0x6930