LLM4Binary/decompile-bench-makefile huggingface dataset:
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/jkOwnLib/gfBlatLib.c
// Function: getHitsFromServer
struct gfHit *getHitsFromServer(int conn, struct lm *lm)
/* Read a lone line of hits from server. */
{
char *s, *line, *q, *t;
struct gfHit *hitList = NULL, *hit;
s = line = netRecieveLongString(conn);
for (;;)
    {
    if ((q = nextWord(&line)) == NULL)
	 break;
    if ((t = nextWord(&line)) == NULL)
	 internalErr();
    lmAllocVar(lm, hit);
    hit->qStart = sqlUnsigned(q);
    hit->tStart = sqlUnsigned(t);
    slAddHead(&hitList, hit);
    }
freez(&s);
slReverse(&hitList);
return hitList;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x18, %rsp
movq %rsi, %rbx
andq $0x0, (%rsp)
callq 0x2bbda
leaq 0x10(%rsp), %r14
movq %rax, (%r14)
movq %rax, 0x8(%rsp)
xorl %r13d, %r13d
movq %r14, %rdi
callq 0x1e9c1
testq %rax, %rax
je 0xd890
movq %rax, %rbp
movq %r14, %rdi
callq 0x1e9c1
movq %rax, %r15
testq %rax, %rax
jne 0xd85b
leaq 0x6f353(%rip), %rdi     # 0x7cb9b
leaq 0x6f549(%rip), %rsi     # 0x7cd98
movl $0xc7, %edx
xorl %eax, %eax
callq 0x223fb
movq %rbx, %rdi
pushq $0x18
popq %rsi
callq 0x26ff4
movq %rax, %r12
movq %rbp, %rdi
callq 0x35d13
movl %eax, 0x8(%r12)
movq %r15, %rdi
callq 0x35d13
movl %eax, 0xc(%r12)
movq %r13, (%r12)
movq %r12, (%rsp)
movq %r12, %r13
jmp 0xd821
leaq 0x8(%rsp), %rdi
callq 0x28c3d
movq %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/jkOwnLib/gfBlatLib.c
// Function: gfRangesBundle
struct gfRange *gfRangesBundle(struct gfRange *exonList, int maxIntron)
/* Bundle a bunch of 'exons' into plausable 'genes'.  It's
 * not necessary to be precise here.  The main thing is to
 * group together exons that are close to each other in the
 * same target sequence. */
{
struct gfRange *geneList = NULL, *gene = NULL, *lastExon = NULL, *exon, *nextExon;

for (exon = exonList; exon != NULL; exon = nextExon)
    {
    nextExon = exon->next;
    if (lastExon == NULL || !sameString(lastExon->tName, exon->tName) 
	|| exon->t3  != lastExon->t3
        || exon->tStart - lastExon->tEnd > maxIntron)
	{
	AllocVar(gene);
	gene->tStart = exon->tStart;
	gene->tEnd = exon->tEnd;
	gene->tName = cloneString(exon->tName);
	gene->tSeq = exon->tSeq;
	gene->qStart = exon->qStart;
	gene->qEnd = exon->qEnd;
	gene->hitCount = exon->hitCount;
	gene->t3 = exon->t3;
	slAddHead(&gene->components, exon);
	slAddHead(&geneList, gene);
	}
    else
        {
	if (exon->qStart < gene->qStart) gene->qStart = exon->qStart;
	if (exon->qEnd > gene->qEnd) gene->qEnd = exon->qEnd;
	if (exon->tStart < gene->tStart) gene->tStart = exon->tStart;
	if (exon->tEnd > gene->tEnd) gene->tEnd = exon->tEnd;
	gene->hitCount += exon->hitCount;
	slAddTail(&gene->components, exon);
	}
    lastExon = exon;
    }
slReverse(&geneList);
return geneList;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movl %esi, %ebx
movq %rdi, %r12
xorl %ebp, %ebp
xorl %r15d, %r15d
movq %rbp, (%rsp)
leaq 0x28(%rbp), %r13
movq %r15, %r14
movq %r12, %r15
testq %r12, %r12
je 0xd9ab
movq (%r15), %r12
testq %r14, %r14
je 0xd954
movq 0x10(%r14), %rdi
movq 0x10(%r15), %rsi
callq 0x6a50
testl %eax, %eax
jne 0xd954
movq 0x38(%r15), %rax
cmpq 0x38(%r14), %rax
jne 0xd954
movl 0x20(%r15), %eax
movl %eax, %ecx
subl 0x24(%r14), %ecx
cmpl %ebx, %ecx
jg 0xd954
movl 0x8(%r15), %ecx
cmpl 0x8(%rbp), %ecx
jge 0xd920
movl %ecx, 0x8(%rbp)
movl 0xc(%r15), %ecx
cmpl 0xc(%rbp), %ecx
jle 0xd92c
movl %ecx, 0xc(%rbp)
cmpl 0x20(%rbp), %eax
jge 0xd934
movl %eax, 0x20(%rbp)
movl 0x24(%r15), %eax
cmpl 0x24(%rbp), %eax
jle 0xd940
movl %eax, 0x24(%rbp)
movl 0x30(%r15), %eax
addl %eax, 0x30(%rbp)
movq %r13, %rdi
movq %r15, %rsi
callq 0x1c502
jmp 0xd8d4
pushq $0x48
popq %rdi
callq 0x28bb0
movq %rax, %r13
movq 0x20(%r15), %rax
movq %rax, 0x20(%r13)
movq 0x10(%r15), %rdi
callq 0x1c306
movq %rax, 0x10(%r13)
movq 0x18(%r15), %rax
movq %rax, 0x18(%r13)
movq 0x8(%r15), %rax
movq %rax, 0x8(%r13)
movl 0x30(%r15), %eax
movl %eax, 0x30(%r13)
movq 0x38(%r15), %rax
movq %rax, 0x38(%r13)
movq 0x28(%r13), %rax
movq %rax, (%r15)
movq %r15, 0x28(%r13)
movq %rbp, (%r13)
movq %r13, %rbp
jmp 0xd8cc
movq %rsp, %rbx
movq %rbx, %rdi
callq 0x1c567
movq (%rbx), %rax
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/jkOwnLib/gfBlatLib.c
// Function: gfFileCacheFree
void gfFileCacheFree(struct hash **pCache)
/* Free up resources in cache. */
{
struct hash *cache = *pCache;
if (cache != NULL)
    {
    hashTraverseEls(cache, gfFileCacheFreeEl);
    hashFree(pCache);
    }
}

// Assembly:
pushq %rbx
movq %rdi, %rbx
movq (%rdi), %rdi
testq %rdi, %rdi
je 0xd9f3
leaq 0x10(%rip), %rsi        # 0xd9f5
callq 0x24728
movq %rbx, %rdi
popq %rbx
jmp 0x2494c
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/jkOwnLib/gfBlatLib.c
// Function: gfFileCacheFreeEl
static void gfFileCacheFreeEl(struct hashEl *el)
/* Free up one file cache info. */
{
char *name = el->name;
if (nibIsFile(name))
    {
    struct nibInfo *nib = el->val;
    nibInfoFree(&nib);
    }
else
    {
    struct twoBitFile *tbf = el->val;
    twoBitClose(&tbf);
    }
el->val = NULL;
}

// Assembly:
pushq %rbx
subq $0x10, %rsp
movq %rdi, %rbx
movq 0x8(%rdi), %rdi
callq 0x2ce73
testl %eax, %eax
je 0xda1d
movq 0x10(%rbx), %rax
leaq 0x8(%rsp), %rdi
movq %rax, (%rdi)
callq 0x2cf59
jmp 0xda2e
movq 0x10(%rbx), %rax
leaq 0x8(%rsp), %rdi
movq %rax, (%rdi)
callq 0x3833b
andq $0x0, 0x10(%rbx)
addq $0x10, %rsp
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/jkOwnLib/gfBlatLib.c
// Function: getTargetName
static void getTargetName(char *tSpec, boolean includeFile, char *targetName)
/* Put sequence name, optionally prefixed by file: in targetName. */
{
if (includeFile)
    {
    char seqName[128];
    char fileName[PATH_LEN];
    gfiGetSeqName(tSpec, seqName, fileName);
    safef(targetName, PATH_LEN, "%s:%s", fileName, seqName);
    }
else
    gfiGetSeqName(tSpec, targetName, NULL);
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
subq $0x280, %rsp            # imm = 0x280
movq %rdx, %rbx
testl %esi, %esi
je 0xdce2
movq %rsp, %r14
leaq 0x80(%rsp), %r15
movq %r14, %rsi
movq %r15, %rdx
callq 0x10a5e
leaq 0x73cf9(%rip), %rdx     # 0x819b9
movq %rbx, %rdi
movl $0x200, %esi            # imm = 0x200
movq %r15, %rcx
movq %r14, %r8
xorl %eax, %eax
callq 0x1fab2
addq $0x280, %rsp            # imm = 0x280
popq %rbx
popq %r14
popq %r15
retq
movq %rbx, %rsi
xorl %edx, %edx
addq $0x280, %rsp            # imm = 0x280
popq %rbx
popq %r14
popq %r15
jmp 0x10a5e
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/jkOwnLib/gfBlatLib.c
// Function: alignComponents
static boolean alignComponents(struct gfRange *combined, struct ssBundle *bun, 
	enum ffStringency stringency)
/* Align each piece of combined->components and put result in
 * bun->ffList. */
{
struct gfRange *range;
struct dnaSeq *qSeq = bun->qSeq, *tSeq = bun->genoSeq;
struct ssFfItem *ffi;
struct ffAli *ali;
int qStart, qEnd, tStart, tEnd;
int extra = 250;
boolean gotAny = FALSE;

for (range = combined->components; range != NULL; range = range->next)
    {
    /* Expand to include some extra sequence around range. */
    qStart = range->qStart - extra;
    tStart = range->tStart - extra;
    qEnd = range->qEnd + extra;
    tEnd = range->tEnd + extra;
    if (range == combined->components)
	{
        qStart -= extra;
	tStart -= extra;
	}
    if (range->next == NULL)
        {
	qEnd += extra;
	tEnd += extra;
	}
    if (qStart < combined->qStart) qStart = combined->qStart;
    if (tStart < combined->tStart) tStart = combined->tStart;
    if (qEnd > combined->qEnd) qEnd = combined->qEnd;
    if (tEnd > combined->tEnd) tEnd = combined->tEnd;
    ali = ffFind(qSeq->dna + qStart,
                 qSeq->dna + qEnd,
		 tSeq->dna + tStart - combined->tStart,
		 tSeq->dna + tEnd - combined->tStart,
		 stringency);
    if (ali != NULL)
        {
	AllocVar(ffi);
	ffi->ff = ali;
	slAddHead(&bun->ffList, ffi);
	gotAny = TRUE;
	}
    }
return gotAny;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %rsi, %rbx
movq %rdi, %r14
movq 0x10(%rsi), %r13
movq 0x18(%rsi), %r15
leaq 0x28(%rdi), %rbp
movq (%rbp), %rbp
testq %rbp, %rbp
je 0xddd2
cmpq 0x28(%r14), %rbp
movl $0xffffff06, %eax       # imm = 0xFFFFFF06
movl $0xfffffe0c, %ecx       # imm = 0xFFFFFE0C
cmovel %ecx, %eax
movl 0x8(%rbp), %edx
addl %eax, %edx
addl 0x20(%rbp), %eax
cmpq $0x0, (%rbp)
movl $0xfa, %ecx
movl $0x1f4, %esi            # imm = 0x1F4
cmovel %esi, %ecx
movl 0xc(%rbp), %esi
addl %ecx, %esi
addl 0x24(%rbp), %ecx
movl 0x8(%r14), %edi
cmpl %edi, %edx
cmovlel %edi, %edx
movslq 0x20(%r14), %r8
cmpl %r8d, %eax
cmovlel %r8d, %eax
movl 0xc(%r14), %edi
cmpl %edi, %esi
cmovgel %edi, %esi
movl 0x24(%r14), %edi
cmpl %edi, %ecx
cmovgel %edi, %ecx
movq 0x10(%r13), %r9
movslq %edx, %rdi
addq %r9, %rdi
movslq %esi, %rsi
addq %r9, %rsi
movq 0x10(%r15), %r9
movslq %eax, %rdx
addq %r9, %rdx
subq %r8, %rdx
movslq %ecx, %rcx
addq %r9, %rcx
subq %r8, %rcx
pushq $0x1
popq %r8
callq 0x9254
testq %rax, %rax
je 0xdd15
movq %rax, %r12
pushq $0x10
popq %rdi
callq 0x28bb0
movq %r12, 0x8(%rax)
movq 0x8(%rbx), %rcx
movq %rcx, (%rax)
movq %rax, 0x8(%rbx)
jmp 0xdd15
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/jkOwnLib/gfBlatLib.c
// Function: saveAlignments
static void saveAlignments(char *chromName, int chromSize, int chromOffset, 
	struct ssBundle *bun, struct hash *t3Hash, 
	boolean qIsRc, boolean tIsRc,
	enum ffStringency stringency, int minMatch, struct gfOutput *out)
/* Save significant alignments to file in .psl format. */
{
struct dnaSeq *tSeq = bun->genoSeq, *qSeq = bun->qSeq;
struct ssFfItem *ffi;
for (ffi = bun->ffList; ffi != NULL; ffi = ffi->next)
    {
    struct ffAli *ff = ffi->ff;
    struct trans3 *t3List = NULL;
    int score;
    if (t3Hash != NULL)
	t3List = hashMustFindVal(t3Hash, tSeq->name);
    score = scoreAli(ff, bun->isProt, stringency, tSeq, t3List);
    if (score >= minMatch)
	{
	out->out(chromName, chromSize, chromOffset, ff, tSeq, t3Hash, qSeq, 
	    qIsRc, tIsRc, stringency, minMatch, out);
	}
    }
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x58, %rsp
movq %r9, 0x30(%rsp)
movq %r8, %rbx
movl %edx, 0x14(%rsp)
movl %esi, 0x10(%rsp)
movq %rdi, 0x28(%rsp)
movq 0x10(%rcx), %rax
movq %rax, 0x20(%rsp)
movq 0x18(%rcx), %rax
movq %rax, 0x8(%rsp)
movq %rcx, 0x38(%rsp)
leaq 0x8(%rcx), %r14
movq %r8, 0x40(%rsp)
movq 0x8(%rsp), %r13
movq (%r14), %r14
testq %r14, %r14
je 0xdf61
movq %r14, 0x50(%rsp)
movq 0x8(%r14), %rbp
testq %rbx, %rbx
je 0xde59
movq 0x8(%rsp), %rax
movq 0x8(%rax), %rsi
movq %rbx, %rdi
callq 0x2447a
movq %rax, %r15
jmp 0xde5c
xorl %r15d, %r15d
movq 0x38(%rsp), %rax
cmpl $0x0, 0x30(%rax)
leaq 0x134d8(%rip), %rax     # 0x21344
movq %rax, 0x18(%rsp)
jne 0xde7f
leaq 0x1349d(%rip), %rax     # 0x21317
movq %rax, 0x18(%rsp)
xorl %ebx, %ebx
movq %rbp, 0x48(%rsp)
testq %rbp, %rbp
je 0xdef3
movq %rbp, %r12
movq 0x8(%rbp), %rbp
movq 0x10(%r12), %rdi
movq 0x20(%r12), %rsi
movl 0x18(%r12), %edx
subl %edi, %edx
callq *0x18(%rsp)
addl %eax, %ebx
testq %rbp, %rbp
je 0xde86
movq 0x20(%rbp), %rdi
movq %r13, %rsi
movq %r15, %rdx
xorl %ecx, %ecx
callq 0x13107
movl %eax, %r14d
movq 0x28(%r12), %rdi
movq %r13, %rsi
movq %r15, %rdx
pushq $0x1
popq %rcx
callq 0x13107
subl %eax, %r14d
movl 0x10(%rbp), %esi
subl 0x18(%r12), %esi
movl %r14d, %edi
movl 0x98(%rsp), %edx
callq 0x2391e
subl %eax, %ebx
jmp 0xde86
movl 0xa0(%rsp), %eax
cmpl %eax, %ebx
movq 0x40(%rsp), %rbx
movq 0x50(%rsp), %r14
jl 0xde29
movq 0x28(%rsp), %rdi
movl 0x10(%rsp), %esi
movl 0x14(%rsp), %edx
movq 0x48(%rsp), %rcx
movq 0x8(%rsp), %r8
movq %rbx, %r9
movq 0xa8(%rsp), %rax
pushq %rax
movl 0xa8(%rsp), %r10d
pushq %r10
movl 0xa8(%rsp), %r10d
pushq %r10
movl 0xa8(%rsp), %r10d
pushq %r10
pushq 0x50(%rsp)
pushq 0x48(%rsp)
callq *0x10(%rax)
addq $0x30, %rsp
jmp 0xde29
addq $0x58, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/jkOwnLib/gfBlatLib.c
// Function: clumpTargetName
char *clumpTargetName(struct gfClump *clump)
/* Return target name of clump - whether it is in memory or on disk. */
{
struct gfSeqSource *target = clump->target;
char *name;
if (target->seq != NULL)
    name = target->seq->name;
else
    name = target->fileName;
if (name == NULL)
    internalErr();
return name;
}

// Assembly:
pushq %rbx
movq 0x10(%rdi), %rax
movq 0x10(%rax), %rcx
testq %rcx, %rcx
cmoveq %rax, %rcx
movq 0x8(%rcx), %rbx
testq %rbx, %rbx
jne 0xdfa3
leaq 0x6ec0b(%rip), %rdi     # 0x7cb9b
leaq 0x6ee01(%rip), %rsi     # 0x7cd98
movl $0x251, %edx            # imm = 0x251
xorl %eax, %eax
callq 0x223fb
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/jkOwnLib/gfBlatLib.c
// Function: gfRangesToFfItem
struct ssFfItem *gfRangesToFfItem(struct gfRange *rangeList, aaSeq *qSeq)
/* Convert ranges to ssFfItem's. */
{
AA *q = qSeq->dna;
struct ffAli *ffList = NULL, *ff;
struct gfRange *range;
struct ssFfItem *ffi;

for (range = rangeList; range != NULL; range = range->next)
    {
    aaSeq *tSeq = range->tSeq;
    AA *t = tSeq->dna;
    AllocVar(ff);
    ff->nStart = q + range->qStart;
    ff->nEnd = q + range->qEnd;
    ff->hStart = t + range->tStart;
    ff->hEnd = t + range->tEnd;
    ff->left = ffList;
    ffList = ff;
    }
AllocVar(ffi);
ffi->ff = ffMakeRightLinks(ffList);
return ffi;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
movq %rdi, %r14
movq 0x10(%rsi), %r12
xorl %ebx, %ebx
pushq $0x38
popq %r15
testq %r14, %r14
je 0xe00a
movq 0x18(%r14), %rax
movq 0x10(%rax), %r13
movq %r15, %rdi
callq 0x28bb0
movslq 0x8(%r14), %rcx
addq %r12, %rcx
movq %rcx, 0x10(%rax)
movslq 0xc(%r14), %rcx
addq %r12, %rcx
movq %rcx, 0x18(%rax)
movslq 0x20(%r14), %rcx
addq %r13, %rcx
movq %rcx, 0x20(%rax)
movslq 0x24(%r14), %rcx
addq %r13, %rcx
movq %rcx, 0x28(%rax)
movq %rbx, (%rax)
movq (%r14), %r14
movq %rax, %rbx
jmp 0xdfbe
pushq $0x10
popq %rdi
callq 0x28bb0
movq %rax, %r14
movq %rbx, %rdi
callq 0x236b0
movq %rax, 0x8(%r14)
movq %r14, %rax
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/jkOwnLib/gfBlatLib.c
// Function: rangeScore
int rangeScore(struct gfRange *range, struct dnaSeq *qSeq)
/* Return score associated with range. */
{
struct gfRange *comp;
struct dnaSeq *tSeq;
int score = 0;
for (comp = range->components; comp != NULL; comp = comp->next)
    {
    tSeq = comp->tSeq;
    score += dnaScoreMatch(tSeq->dna + range->tStart, qSeq->dna + range->qStart, 
        range->tEnd - range->tStart);
    if (comp->next != NULL)
        score -= 4;
    }
return score;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
movq %rsi, %rbx
movq %rdi, %r14
movq 0x28(%rdi), %r12
xorl %r15d, %r15d
testq %r12, %r12
je 0xe1b7
movq 0x18(%r12), %rax
movslq 0x20(%r14), %rcx
movq %rcx, %rdi
addq 0x10(%rax), %rdi
movl 0x24(%r14), %edx
subl %ecx, %edx
movslq 0x8(%r14), %rsi
addq 0x10(%rbx), %rsi
callq 0x21317
leal (%rax,%r15), %ecx
movq (%r12), %r12
testq %r12, %r12
leal -0x4(%rax,%r15), %r15d
cmovel %ecx, %r15d
jmp 0xe179
movl %r15d, %eax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/jkOwnLib/gfBlatLib.c
// Function: rangeCoorTimes3
void rangeCoorTimes3(struct gfRange *rangeList)
/* Multiply coordinates on range list times three (to go from
 * amino acid to nucleotide. */
{
struct gfRange *range;
for (range = rangeList; range != NULL; range = range->next)
    {
    range->qStart *= 3;
    range->qEnd *= 3;
    range->tStart = range->tStart*3;
    range->tEnd = range->tEnd*3;
    }
}

// Assembly:
testq %rdi, %rdi
je 0xe755
imull $0x3, 0x8(%rdi), %eax
movl %eax, 0x8(%rdi)
imull $0x3, 0xc(%rdi), %eax
movl %eax, 0xc(%rdi)
imull $0x3, 0x20(%rdi), %eax
movl %eax, 0x20(%rdi)
imull $0x3, 0x24(%rdi), %eax
movl %eax, 0x24(%rdi)
movq (%rdi), %rdi
jmp 0xe72f
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/jkOwnLib/gfBlatLib.c
// Function: seqClumpToRangeList
static struct gfRange *seqClumpToRangeList(struct gfClump *clumpList, int frame)
/* Convert from clump list to range list. */
{
struct gfRange *rangeList = NULL, *range;
struct gfClump *clump;
char *name;
int tOff;

for (clump = clumpList; clump != NULL; clump = clump->next)
    {
    tOff = clump->target->start;
    AllocVar(range);
    range->qStart = clump->qStart;
    range->qEnd = clump->qEnd;
    name = clumpTargetName(clump);
    range->tName = cloneString(name);
    range->tStart = clump->tStart - tOff;
    range->tEnd = clump->tEnd - tOff;
    range->tSeq = clump->target->seq;
    range->frame = frame;
    slAddHead(&rangeList, range);
    }
slReverse(&rangeList);
return rangeList;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x20, %rsp
andq $0x0, 0x8(%rsp)
movl %esi, %ebx
movq %rdi, %r14
xorl %r13d, %r13d
pushq $0x48
popq %r15
testq %r14, %r14
je 0xedd0
movq 0x10(%r14), %rax
movss 0x18(%rax), %xmm0
movaps %xmm0, 0x10(%rsp)
movq %r15, %rdi
callq 0x28bb0
movq %rax, %r12
movq 0x8(%r14), %rax
movq %rax, 0x8(%r12)
movq %r14, %rdi
callq 0xdf70
movq %rax, %rdi
callq 0x1c306
movq %rax, 0x10(%r12)
movq 0x18(%r14), %xmm0
pshufd $0x50, 0x10(%rsp), %xmm1 # xmm1 = mem[0,0,1,1]
psubd %xmm1, %xmm0
movq %xmm0, 0x20(%r12)
movq 0x10(%r14), %rax
movq 0x10(%rax), %rax
movq %rax, 0x18(%r12)
movl %ebx, 0x34(%r12)
movq %r13, (%r12)
movq %r12, 0x8(%rsp)
movq (%r14), %r14
movq %r12, %r13
jmp 0xed59
leaq 0x8(%rsp), %rbx
movq %rbx, %rdi
callq 0x1c567
movq (%rbx), %rax
addq $0x20, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/jkOwnLib/gfBlatLib.c
// Function: loadHashT3Ranges
static void loadHashT3Ranges(struct gfRange *rangeList, 
	char *tSeqDir, struct hash *tFileCache, int qSeqSize, boolean isRc, 
	struct hash **retT3Hash, struct dnaSeq **retSeqList,
	struct slRef **retT3RefList)
/* Load DNA in ranges into memory, and put translation in a hash
 * that gets returned. */
{
struct hash *t3Hash = newHash(10);
struct dnaSeq *targetSeq, *tSeqList = NULL;
struct slRef *t3RefList = NULL;
struct gfRange *range;

for (range = rangeList; range != NULL; range = range->next)
    {
    struct trans3 *t3, *oldT3;

    targetSeq = gfiExpandAndLoadCached(range, tFileCache,
    	tSeqDir, qSeqSize*3, &range->tTotalSize, TRUE, isRc, usualExpansion);
    slAddHead(&tSeqList, targetSeq);
    freez(&targetSeq->name);
    targetSeq->name = cloneString(range->tName);
    t3 = trans3New(targetSeq);
    refAdd(&t3RefList, t3);
    t3->start = range->tStart;
    t3->end = range->tEnd;
    t3->nibSize = range->tTotalSize;
    t3->isRc = isRc;
    if ((oldT3 = hashFindVal(t3Hash, range->tName)) != NULL)
	{
	slAddTail(&oldT3->next, t3);
	}
    else
	{
	hashAdd(t3Hash, range->tName, t3);
	}
    }
*retT3Hash = t3Hash;
*retSeqList = tSeqList;
*retT3RefList = t3RefList;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x28, %rsp
movq %r9, 0x10(%rsp)
movl %r8d, %r14d
movl %ecx, %ebx
movq %rdx, 0x20(%rsp)
movq %rsi, 0x18(%rsp)
movq %rdi, %r13
pushq $0xa
popq %rdi
pushq $0x1
popq %rsi
callq 0x245c9
leaq 0x8(%rsp), %rcx
andq $0x0, (%rcx)
movq %rax, %rbp
leal (%rbx,%rbx,2), %ebx
xorl %r12d, %r12d
testq %r13, %r13
je 0xeee2
leaq 0x40(%r13), %r8
movq %r13, %rdi
movq 0x20(%rsp), %rsi
movq 0x18(%rsp), %rdx
movl %ebx, %ecx
pushq $0x1
popq %r9
pushq $0x1f4                  # imm = 0x1F4
pushq %r14
callq 0x10845
popq %rcx
popq %rdx
movq %rax, %r15
movq %r12, (%rax)
leaq 0x8(%rax), %rdi
callq 0x28c3d
movq 0x10(%r13), %rdi
callq 0x1c306
movq %rax, 0x8(%r15)
movq %r15, %rdi
callq 0x12f80
movq %rax, %r12
leaq 0x8(%rsp), %rdi
movq %rax, %rsi
callq 0x1d218
movq 0x20(%r13), %rax
movq %rax, 0x30(%r12)
movl 0x40(%r13), %eax
movl %eax, 0x38(%r12)
movl %r14d, 0x3c(%r12)
movq 0x10(%r13), %rsi
movq %rbp, %rdi
callq 0x244c6
testq %rax, %rax
je 0xeec7
movq %rax, %rdi
movq %r12, %rsi
callq 0x1c502
jmp 0xeed6
movq 0x10(%r13), %rsi
movq %rbp, %rdi
movq %r12, %rdx
callq 0x242d0
movq (%r13), %r13
movq %r15, %r12
jmp 0xee30
movq 0x10(%rsp), %rax
movq %rbp, (%rax)
movq 0x60(%rsp), %rax
movq %r12, (%rax)
movq 0x8(%rsp), %rax
movq 0x68(%rsp), %rcx
movq %rax, (%rcx)
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/jkOwnLib/gfBlatLib.c
// Function: untranslateRangeList
void untranslateRangeList(struct gfRange *rangeList, int qFrame, int tFrame, 
	struct hash *t3Hash, struct trans3 *t3, int tOffset)
/* Translate coordinates from protein to dna. */
{
struct gfRange *range;
for (range = rangeList; range != NULL; range = range->next)
    {
    range->qStart = 3*range->qStart + qFrame;
    range->qEnd = 3*range->qEnd + qFrame;
    range->tStart = 3*range->tStart + tFrame;
    range->tEnd = 3*range->tEnd + tFrame;
    if (t3Hash)
	t3 = trans3Find(t3Hash, range->tSeq->name, range->tStart + tOffset, range->tEnd + tOffset);
    range->tSeq = t3->seq;
    range->t3 = t3;
    }
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
movl %r9d, %ebx
movq %r8, %rax
movq %rcx, %r14
movl %edx, %ebp
movl %esi, %r15d
movq %rdi, %r12
testq %r12, %r12
je 0xef90
imull $0x3, 0x8(%r12), %esi
addl %r15d, %esi
imull $0x3, 0xc(%r12), %edi
addl %r15d, %edi
imull $0x3, 0x20(%r12), %edx
addl %ebp, %edx
imull $0x3, 0x24(%r12), %ecx
addl %ebp, %ecx
movl %esi, 0x8(%r12)
movl %edi, 0xc(%r12)
movl %edx, 0x20(%r12)
movl %ecx, 0x24(%r12)
testq %r14, %r14
je 0xef7c
movq 0x18(%r12), %rax
movq 0x8(%rax), %rsi
addl %ebx, %edx
addl %ebx, %ecx
movq %r14, %rdi
callq 0x13060
movq 0x10(%rax), %rcx
movq %rcx, 0x18(%r12)
movq %rax, 0x38(%r12)
movq (%r12), %r12
jmp 0xef27
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/jkOwnLib/gfBlatLib.c
// Function: addToBigBundleList
static void addToBigBundleList(struct ssBundle **pOneList, struct hash *bunHash, 
	struct ssBundle **pBigList, struct dnaSeq *query)
/* Add bundles in one list to bigList, consolidating bundles that refer
 * to the same target sequence.  This will destroy oneList in the process. */
{
struct ssBundle *oneBun, *bigBun;

for (oneBun = *pOneList; oneBun != NULL; oneBun = oneBun->next)
    {
    char *name = oneBun->genoSeq->name;
    if ((bigBun = hashFindVal(bunHash, name)) == NULL)
        {
	AllocVar(bigBun);
	slAddHead(pBigList, bigBun);
	hashAdd(bunHash, name, bigBun);
	bigBun->qSeq = query;
	bigBun->genoSeq = oneBun->genoSeq;
	bigBun->isProt = oneBun->isProt;
	bigBun->avoidFuzzyFindKludge = oneBun->avoidFuzzyFindKludge;
	}
    bigBun->ffList = slCat(bigBun->ffList, oneBun->ffList);
    oneBun->ffList = NULL;
    }
ssBundleFreeList(pOneList);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %rcx, %rbx
movq %rdx, %r14
movq %rsi, %r12
movq %rdi, %r13
movq %rdi, (%rsp)
movq (%r13), %r13
testq %r13, %r13
je 0xfd64
movq 0x18(%r13), %rax
movq 0x8(%rax), %r15
movq %r12, %rdi
movq %r15, %rsi
callq 0x244c6
movq %rax, %rbp
testq %rax, %rax
jne 0xfd4c
pushq $0x48
popq %rdi
callq 0x28bb0
movq %rax, %rbp
movq (%r14), %rax
movq %rax, (%rbp)
movq %rbp, (%r14)
movq %r12, %rdi
movq %r15, %rsi
movq %rbp, %rdx
callq 0x242d0
movq %rbx, 0x10(%rbp)
movq 0x18(%r13), %rax
movq %rax, 0x18(%rbp)
movl 0x30(%r13), %eax
movl %eax, 0x30(%rbp)
movl 0x40(%r13), %eax
movl %eax, 0x40(%rbp)
movq 0x8(%rbp), %rdi
movq 0x8(%r13), %rsi
callq 0x1c549
movq %rax, 0x8(%rbp)
andq $0x0, 0x8(%r13)
jmp 0xfceb
movq (%rsp), %rdi
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
jmp 0x11cd5
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/jkOwnLib/gfBlatLib.c
// Function: startSeqQuery
static void startSeqQuery(int conn, bioSeq *seq, char *type)
/* Send a query that involves some sequence. */
{
char buf[256];
sprintf(buf, "%s%s %d", gfSignature(), type, seq->size);
mustWriteFd(conn, buf, strlen(buf));
if (read(conn, buf, 1) < 0)
    errAbort("startSeqQuery: read failed: %s", strerror(errno));
if (buf[0] != 'Y')
    errAbort("Expecting 'Y' from server, got %c", buf[0]);
mustWriteFd(conn, seq->dna, seq->size);
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
subq $0x108, %rsp            # imm = 0x108
movq %rdx, %r15
movq %rsi, %r14
movl %edi, %ebx
xorl %eax, %eax
callq 0xa87c
movl 0x18(%r14), %r8d
leaq 0x6cca6(%rip), %rsi     # 0x7cddf
movq %rsp, %r12
movq %r12, %rdi
movq %rax, %rdx
movq %r15, %rcx
xorl %eax, %eax
callq 0x6170
movq %r12, %rdi
callq 0x62d0
movl %ebx, %edi
movq %r12, %rsi
movq %rax, %rdx
callq 0x1f108
pushq $0x1
popq %rdx
movl %ebx, %edi
movq %r12, %rsi
callq 0x6aa0
testq %rax, %rax
jns 0x10190
callq 0x6060
movl (%rax), %edi
callq 0x6230
leaq 0x6cc61(%rip), %rdi     # 0x7cde7
movq %rax, %rsi
xorl %eax, %eax
callq 0x223fb
movsbl (%rsp), %esi
cmpl $0x59, %esi
je 0x101a7
leaq 0x6cc66(%rip), %rdi     # 0x7ce06
xorl %eax, %eax
callq 0x223fb
movq 0x10(%r14), %rsi
movslq 0x18(%r14), %rdx
movl %ebx, %edi
callq 0x1f108
addq $0x108, %rsp            # imm = 0x108
popq %rbx
popq %r12
popq %r14
popq %r15
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/jkOwnLib/gfBlatLib.c
// Function: findTileSize
static int findTileSize(char *line)
/* Parse through line/val pairs looking for tileSize. */
{
char *var, *val;
int tileSize = 4;
for (;;)
    {
    var = nextWord(&line);
    if (var == NULL)
         break;
    val = nextWord(&line);
    if (val == NULL)
	 {
	 internalErr();
         break;
	 }
    if (sameString("tileSize", var))
         {
	 tileSize = atoi(val);
	 if (tileSize <= 0)
	     internalErr();
	 }
    }
return tileSize;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %rsp, %r14
movq %rdi, (%r14)
pushq $0x4
popq %rbx
leaq 0x6c1ed(%rip), %r15     # 0x7c3e2
leaq 0x6cb9c(%rip), %r13     # 0x7cd98
movq %r14, %rdi
callq 0x1e9c1
testq %rax, %rax
je 0x1026b
movq %rax, %r12
movq %r14, %rdi
callq 0x1e9c1
testq %rax, %rax
je 0x10251
movq %rax, %rbp
movq %r15, %rdi
movq %r12, %rsi
callq 0x6a50
testl %eax, %eax
jne 0x101fc
movq %rbp, %rdi
callq 0x6bd0
movl %eax, %ebx
testl %eax, %eax
jg 0x101fc
leaq 0x6c95b(%rip), %rdi     # 0x7cb9b
movq %r13, %rsi
movl $0xb6, %edx
xorl %eax, %eax
callq 0x223fb
jmp 0x101fc
leaq 0x6c943(%rip), %rdi     # 0x7cb9b
leaq 0x6cb39(%rip), %rsi     # 0x7cd98
movl $0xaf, %edx
xorl %eax, %eax
callq 0x223fb
movl %ebx, %eax
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/jkOwnLib/gfClientLib.c
// Function: gfClientFileArray
void gfClientFileArray(char *fileName, char ***retFiles, int *retFileCount)
/* Check if file if .2bit or .nib or .fa.  If so return just that
 * file in a list of one.  Otherwise read all file and treat file
 * as a list of filenames.  */
{
boolean gotSingle = FALSE;
char *buf;		/* This will leak memory but won't matter. */

if (nibIsFile(fileName) || twoBitIsSpec(fileName)
    || sameString(fileName, "stdin")
    || endsWith(fileName, ".Z")
    || endsWith(fileName, ".gz")
    || endsWith(fileName, ".bz2"))
    gotSingle = TRUE;
/* Detect .fa files (where suffix is not standardized)
 * by first character being a '>'. */
else
    {
    FILE *f = mustOpen(fileName, "r");
    char c = fgetc(f);
    fclose(f);
    if (c == '>')
        gotSingle = TRUE;
    }
if (gotSingle)
    {
    char **files;
    *retFiles = AllocArray(files, 1);
    files[0] = cloneString(fileName);
    *retFileCount = 1;
    return;
    }
else
    {
    readAllWords(fileName, retFiles, retFileCount, &buf);
    }
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
subq $0x10, %rsp
movq %rdx, %rbx
movq %rsi, %r15
movq %rdi, %r14
callq 0x2ce73
testl %eax, %eax
jne 0x102a6
movq %r14, %rdi
callq 0x391eb
testl %eax, %eax
je 0x102d3
pushq $0x8
popq %rdi
callq 0x28a1f
movq %rax, %r12
movq %rax, (%r15)
movq %r14, %rdi
callq 0x1c306
movq %rax, (%r12)
movl $0x1, (%rbx)
addq $0x10, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq
leaq 0x7271f(%rip), %rsi     # 0x829f9
movq %r14, %rdi
callq 0x6a50
testl %eax, %eax
je 0x102a6
leaq 0x6cd63(%rip), %rsi     # 0x7d050
movq %r14, %rdi
callq 0x1de0f
testl %eax, %eax
jne 0x102a6
leaq 0x77336(%rip), %rsi     # 0x87636
movq %r14, %rdi
callq 0x1de0f
testl %eax, %eax
jne 0x102a6
leaq 0x6cd40(%rip), %rsi     # 0x7d053
movq %r14, %rdi
callq 0x1de0f
testl %eax, %eax
jne 0x102a6
leaq 0x74ae3(%rip), %rsi     # 0x84e09
movq %r14, %rdi
callq 0x1ec79
movq %rax, %r12
movq %rax, %rdi
callq 0x6bf0
movl %eax, %ebp
movq %r12, %rdi
callq 0x66e0
cmpb $0x3e, %bpl
je 0x102a6
leaq 0x8(%rsp), %rcx
movq %r14, %rdi
movq %r15, %rsi
movq %rbx, %rdx
callq 0x2d19d
jmp 0x102c6
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/jkOwnLib/gfInternal.c
// Function: gfiExpandRange
void gfiExpandRange(struct gfRange *range, int qSize, int tSize, 
	boolean respectFrame, boolean isRc, int expansion)
/* Expand range to cover an additional 500 bases on either side. */
{
int x;

x = range->qStart - expansion;
if (x < 0) x = 0;
range->qStart = x;

x = range->qEnd + expansion;
if (x > qSize) x = qSize;
range->qEnd = x;

x = range->tStart - expansion;
if (x < 0) x = 0;
if (respectFrame && !isRc) 
    {
    x = extendRespect(range->tStart, x);
    }
range->tStart = x;

x = range->tEnd + expansion;
if (x > tSize) x = tSize;
if (respectFrame && isRc)
    {
    x = extendRespect(range->tEnd, x);
    if (x > tSize)
        x -= 3;
    }
range->tEnd = x;
}

// Assembly:
pushq %rbx
movl %edx, %r10d
movl 0x8(%rdi), %edx
movl 0x20(%rdi), %eax
subl %r9d, %edx
xorl %r11d, %r11d
testl %edx, %edx
cmovlel %r11d, %edx
movl %edx, 0x8(%rdi)
movl 0xc(%rdi), %edx
addl %r9d, %edx
cmpl %esi, %edx
cmovgel %esi, %edx
movl %edx, 0xc(%rdi)
movl %eax, %esi
subl %r9d, %esi
testl %esi, %esi
cmovlel %r11d, %esi
testl %ecx, %ecx
sete %dl
testl %r8d, %r8d
setne %r11b
orb %dl, %r11b
movl $0x3, %ebx
jne 0x10805
cltd
idivl %ebx
movl %edx, %r11d
movl %esi, %eax
xorl %edx, %edx
divl %ebx
addl %esi, %r11d
subl %edx, %r11d
movl %r11d, %esi
testl %r8d, %r8d
sete %dl
movl %esi, 0x20(%rdi)
movl 0x24(%rdi), %eax
addl %eax, %r9d
cmpl %r10d, %r9d
cmovgel %r10d, %r9d
testl %ecx, %ecx
sete %cl
orb %dl, %cl
jne 0x1083f
cltd
idivl %ebx
movl %edx, %ecx
movl %r9d, %eax
cltd
idivl %ebx
addl %r9d, %ecx
subl %edx, %ecx
leal -0x3(%rcx), %r9d
cmpl %r10d, %ecx
cmovlel %ecx, %r9d
movl %r9d, 0x24(%rdi)
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/jkOwnLib/gfInternal.c
// Function: gfiGetSeqName
void gfiGetSeqName(char *spec, char *name, char *file)
/* Extract sequence name and optionally file name from spec, 
 * which includes nib and 2bit files.  (The file may be NULL
 * if you don't care.) */
{
if (nibIsFile(spec))
    {
    splitPath(spec, NULL, name, NULL);
    if (file != NULL)
        strcpy(file, spec);
    }
else
    {
    char *s = strchr(spec, ':');
    if (s == NULL)
	errAbort("Expecting colon in %s", spec);
    strcpy(name, s+1);
    if (file != NULL)
        {
	int fileNameSize = s - spec;
	memcpy(file, spec, fileNameSize);
	file[fileNameSize] = 0;
	}
    }
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
movq %rdx, %rbx
movq %rsi, %r15
movq %rdi, %r14
callq 0x2ce73
testl %eax, %eax
je 0x10aa2
movq %r14, %rdi
xorl %esi, %esi
movq %r15, %rdx
xorl %ecx, %ecx
callq 0x23b2e
testq %rbx, %rbx
je 0x10af1
movq %rbx, %rdi
movq %r14, %rsi
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
jmp 0x6680
pushq $0x3a
popq %rsi
movq %r14, %rdi
callq 0x6270
movq %rax, %r12
testq %rax, %rax
jne 0x10ac6
leaq 0x6c6e4(%rip), %rdi     # 0x7d1a0
movq %r14, %rsi
xorl %eax, %eax
callq 0x223fb
leaq 0x1(%r12), %rsi
movq %r15, %rdi
callq 0x6680
testq %rbx, %rbx
je 0x10af1
subl %r14d, %r12d
movslq %r12d, %r15
movq %rbx, %rdi
movq %r14, %rsi
movq %r15, %rdx
callq 0x6570
movb $0x0, (%rbx,%r15)
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
nopl (%rax)
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/jkOwnLib/gfOut.c
// Function: gfOutputPsl
struct gfOutput *gfOutputPsl(int goodPpt, 
	boolean qIsProt, boolean tIsProt, FILE *f, 
	boolean saveSeq, boolean noHead)
/* Set up psl/pslx output */
{
struct gfOutput *out = gfOutputInit(goodPpt, qIsProt, tIsProt);
struct pslxData *pslData;

AllocVar(pslData);
pslData->saveSeq = saveSeq;
pslData->f = f;
out->out = pslOut;
out->data = pslData;
if (!noHead)
    out->fileHead = pslHead;
return out;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %rbx
pushq %rax
movl %r9d, %ebp
movl %r8d, %r14d
movq %rcx, %r15
callq 0x10b53
movq %rax, %rbx
pushq $0x10
popq %rdi
callq 0x28bb0
movl %r14d, 0x8(%rax)
movq %r15, (%rax)
leaq 0x47(%rip), %rcx        # 0x10b75
movq %rcx, 0x10(%rbx)
movq %rax, 0x8(%rbx)
testl %ebp, %ebp
jne 0x10b45
leaq 0x60e(%rip), %rax       # 0x1114f
movq %rax, 0x20(%rbx)
movq %rbx, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/jkOwnLib/gfOut.c
// Function: gfOutputInit
static struct gfOutput *gfOutputInit(int goodPpt, boolean qIsProt, boolean tIsProt)
/* Allocate and initialize gfOutput.   You'll need to fill in 
 * gfOutput.out at a minimum, and likely gfOutput.data before
 * using though. */
{
struct gfOutput *out;
AllocVar(out);
out->minGood = goodPpt;
out->qIsProt = qIsProt;
out->tIsProt = tIsProt;
return out;
}

// Assembly:
pushq %rbp
pushq %r14
pushq %rbx
movl %edx, %ebx
movl %esi, %ebp
movl %edi, %r14d
pushq $0x50
popq %rdi
callq 0x28bb0
movl %r14d, 0x38(%rax)
movl %ebp, 0x3c(%rax)
movl %ebx, 0x40(%rax)
popq %rbx
popq %r14
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/jkOwnLib/gfOut.c
// Function: gfOutputAxtMem
struct gfOutput *gfOutputAxtMem(int goodPpt, boolean qIsProt, 
	boolean tIsProt)
/* Setup output for in memory axt output. */
{
struct gfOutput *out = gfOutputInit(goodPpt, qIsProt, tIsProt);
struct axtData *ad;
AllocVar(ad);
out->out = saveAxtBundle;
out->data = ad;
return out;
}

// Assembly:
pushq %rbx
callq 0x10b53
movq %rax, %rbx
pushq $0x30
popq %rdi
callq 0x28bb0
leaq 0xd(%rip), %rcx         # 0x1117c
movq %rcx, 0x10(%rbx)
movq %rax, 0x8(%rbx)
movq %rbx, %rax
popq %rbx
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/jkOwnLib/gfOut.c
// Function: axtQueryOut
static void axtQueryOut(struct gfOutput *out, FILE *f)
/* Do axt oriented output - at end of processing query. */
{
struct axtData *aod = out->data;
struct axtBundle *gab;
for (gab = aod->bundleList; gab != NULL; gab = gab->next)
    {
    struct axt *axt;
    for (axt = gab->axtList; axt != NULL; axt = axt->next)
	axtWrite(axt, f);
    }
axtBundleFreeList(&aod->bundleList);
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
movq %rsi, %rbx
movq 0x8(%rdi), %r14
movq %r14, %r12
movq (%r12), %r12
testq %r12, %r12
je 0x115cf
leaq 0x8(%r12), %r15
movq (%r15), %r15
testq %r15, %r15
je 0x115ac
movq %r15, %rdi
movq %rbx, %rsi
callq 0x16975
jmp 0x115ba
movq %r14, %rdi
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
jmp 0x17d9b
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/jkOwnLib/gfOut.c
// Function: gfOutputMaf
struct gfOutput *gfOutputMaf(int goodPpt, boolean qIsProt, 
	boolean tIsProt, FILE *f)
/* Setup output for maf format. */
{
struct gfOutput *out = gfOutputAxtMem(goodPpt, qIsProt, tIsProt);
out->queryOut = mafQueryOut;
out->fileHead = mafHead;
return out;
}

// Assembly:
pushq %rax
callq 0x11157
leaq 0x11(%rip), %rcx        # 0x11600
movq %rcx, 0x18(%rax)
leaq 0x6e(%rip), %rcx        # 0x11668
movq %rcx, 0x20(%rax)
popq %rcx
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/jkOwnLib/gfOut.c
// Function: mafQueryOut
static void mafQueryOut(struct gfOutput *out, FILE *f)
/* Do axt oriented output - at end of processing query. */
{
struct axtData *aod = out->data;
struct axtBundle *gab;
for (gab = aod->bundleList; gab != NULL; gab = gab->next)
    {
    struct axt *axt;
    for (axt = gab->axtList; axt != NULL; axt = axt->next)
	{
	struct mafAli temp;
	mafFromAxtTemp(axt, gab->tSize, gab->qSize, &temp);
	mafWrite(f, &temp);
	}
    }
axtBundleFreeList(&aod->bundleList);
}

// Assembly:
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x30, %rsp
movq %rsi, %r14
movq 0x8(%rdi), %rbx
leaq 0x8(%rsp), %r15
movq %rbx, %r13
movq (%r13), %r13
testq %r13, %r13
je 0x11652
leaq 0x8(%r13), %r12
movq (%r12), %r12
testq %r12, %r12
je 0x1161c
movl 0x10(%r13), %esi
movl 0x14(%r13), %edx
movq %r12, %rdi
movq %r15, %rcx
callq 0x286fc
movq %r14, %rdi
movq %r15, %rsi
callq 0x27bf6
jmp 0x11629
movq %rbx, %rdi
callq 0x17d9b
addq $0x30, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/jkOwnLib/gfOut.c
// Function: gfOutputSim4
struct gfOutput *gfOutputSim4(int goodPpt, boolean qIsProt, boolean tIsProt, 
	char *databaseName)
/* Set up to output in sim4 format. */
{
struct gfOutput *out = gfOutputAxtMem(goodPpt, qIsProt, tIsProt);
struct axtData *ad = out->data;
if (qIsProt || tIsProt)
    errAbort("sim4 output is not available for protein query sequences.");
ad->databaseName = databaseName;
out->queryOut = sim4QueryOut;
return out;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
movq %rcx, %rbx
movl %edx, %ebp
movl %esi, %r15d
callq 0x11157
movq %rax, %r14
movq 0x8(%rax), %r12
orl %r15d, %ebp
je 0x116a6
leaq 0x6bb29(%rip), %rdi     # 0x7d1c8
xorl %eax, %eax
callq 0x223fb
movq %rbx, 0x8(%r12)
leaq 0x10(%rip), %rax        # 0x116c2
movq %rax, 0x18(%r14)
movq %r14, %rax
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/jkOwnLib/gfOut.c
// Function: sim4QueryOut
static void sim4QueryOut(struct gfOutput *out, FILE *f)
/* Do sim4-like output - at end of processing query. */
{
struct axtData *aod = out->data;
struct axtBundle *gab;
slReverse(&aod->bundleList);

for (gab = aod->bundleList; gab != NULL; gab = gab->next)
    {
    struct axt *axt = gab->axtList;
    // check minIdentity of the entire alignment
    int goodPpt = 1000 * axtListRatio(axt);
    if (!(goodPpt >= out->minGood))
	continue; 
    fprintf(f, "\n");
    fprintf(f, "seq1 = %s, %d bp\n", axt->qName, gab->qSize);
    fprintf(f, "seq2 = %s, %d bp\n", axt->tName, gab->tSize);
    fprintf(f, "\n");
    if (axt->qStrand == '-')
	fprintf(f, "(complement)\n");
    for (; axt != NULL; axt = axt->next)
	{
	fprintf(f, "%d-%d  ", axt->qStart+1, axt->qEnd);
	fprintf(f, "(%d-%d)   ", axt->tStart+1, axt->tEnd);
	fprintf(f, "%1.0f%% ", 100.0 * axtIdRatio(axt));
	if (axt->qStrand == '-')
	     fprintf(f, "<-\n");
	else
	     fprintf(f, "->\n");
	}
    }
axtBundleFreeList(&aod->bundleList);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x18, %rsp
movq %rsi, %rbx
movq %rdi, 0x10(%rsp)
movq 0x8(%rdi), %r14
movq %r14, %rdi
callq 0x1c567
movq %r14, 0x8(%rsp)
movq (%r14), %r14
testq %r14, %r14
je 0x11849
movq 0x8(%r14), %r13
xorl %ebp, %ebp
movq %r13, %r12
xorl %r15d, %r15d
testq %r12, %r12
je 0x1171b
movq %r12, %rdi
callq 0x11abe
addl %eax, %ebp
addl 0x38(%r12), %r15d
movq (%r12), %r12
jmp 0x11701
cvtsi2sd %ebp, %xmm0
cvtsi2sd %r15d, %xmm1
divsd %xmm1, %xmm0
mulsd 0x6ba88(%rip), %xmm0    # 0x7d1b8
cvttsd2si %xmm0, %eax
movq 0x10(%rsp), %rcx
cmpl %eax, 0x38(%rcx)
pushq $0x1
popq %r15
leaq 0x6bc7a(%rip), %r12     # 0x7d3c1
jg 0x116e9
pushq $0xa
popq %rbp
movl %ebp, %edi
movq %rbx, %rsi
callq 0x6930
movq 0x8(%r13), %rdx
movl 0x14(%r14), %ecx
movq %rbx, %rdi
leaq 0x6bc27(%rip), %rsi     # 0x7d38f
xorl %eax, %eax
callq 0x6a90
movq 0x20(%r13), %rdx
movl 0x10(%r14), %ecx
movq %rbx, %rdi
leaq 0x6bc20(%rip), %rsi     # 0x7d3a1
xorl %eax, %eax
callq 0x6a90
movl %ebp, %edi
movq %rbx, %rsi
callq 0x6930
cmpb $0x2d, 0x18(%r13)
jne 0x117ae
leaq 0x6bc13(%rip), %rdi     # 0x7d3b3
pushq $0xd
popq %rsi
movq %r15, %rdx
movq %rbx, %rcx
callq 0x6e70
leaq 0x6bc14(%rip), %rbp     # 0x7d3c9
testq %r13, %r13
je 0x116e9
movl 0x10(%r13), %edx
movl 0x14(%r13), %ecx
incl %edx
movq %rbx, %rdi
movq %r12, %rsi
xorl %eax, %eax
callq 0x6a90
movl 0x28(%r13), %edx
movl 0x2c(%r13), %ecx
incl %edx
movq %rbx, %rdi
movq %rbp, %rsi
xorl %eax, %eax
callq 0x6a90
movq %r13, %rdi
callq 0x11abe
cvtsi2sd %eax, %xmm0
cvtsi2sdl 0x38(%r13), %xmm1
divsd %xmm1, %xmm0
mulsd 0x6b9b6(%rip), %xmm0    # 0x7d1c0
movq %rbx, %rdi
leaq 0x6bbc0(%rip), %rsi     # 0x7d3d4
movb $0x1, %al
callq 0x6a90
cmpb $0x2d, 0x18(%r13)
leaq 0x74222(%rip), %rdi     # 0x85a49
leaq 0x6bbaf(%rip), %rax     # 0x7d3dd
cmoveq %rax, %rdi
pushq $0x3
popq %rsi
movq %r15, %rdx
movq %rbx, %rcx
callq 0x6e70
movq (%r13), %r13
jmp 0x117b5
movq 0x8(%rsp), %rdi
addq $0x18, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
jmp 0x17d9b
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/jkOwnLib/gfOut.c
// Function: gfOutputBlast
struct gfOutput *gfOutputBlast(int goodPpt, 
	boolean qIsProt, boolean tIsProt, 
	char *databaseName, int databaseSeqCount, double databaseLetters,
	char *blastType, double minIdentity, FILE *f)
/* Setup output for blast format. */
{
struct gfOutput *out = gfOutputAxtMem(goodPpt, qIsProt, tIsProt);
struct axtData *ad = out->data;
ad->databaseName = databaseName;
ad->databaseSeqCount = databaseSeqCount;
ad->databaseLetters = databaseLetters;
ad->blastType = blastType;
ad->minIdentity = minIdentity;
out->queryOut = blastQueryOut;
return out;
}

// Assembly:
pushq %rbp
pushq %r14
pushq %rbx
subq $0x10, %rsp
movsd %xmm1, 0x8(%rsp)
movq %r9, %rbx
movsd %xmm0, (%rsp)
movl %r8d, %ebp
movq %rcx, %r14
callq 0x11157
movq 0x8(%rax), %rcx
movq %r14, 0x8(%rcx)
movl %ebp, 0x10(%rcx)
movsd (%rsp), %xmm0
movsd %xmm0, 0x18(%rcx)
movq %rbx, 0x20(%rcx)
movsd 0x8(%rsp), %xmm0
movsd %xmm0, 0x28(%rcx)
leaq 0xd(%rip), %rcx         # 0x118ba
movq %rcx, 0x18(%rax)
addq $0x10, %rsp
popq %rbx
popq %r14
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/jkOwnLib/gfOut.c
// Function: blastQueryOut
static void blastQueryOut(struct gfOutput *out, FILE *f)
/* Output blast on query. */
{
struct axtData *aod = out->data;
axtBlastOut(aod->bundleList, out->queryIx, out->qIsProt, f,
	aod->databaseName, aod->databaseSeqCount, aod->databaseLetters,
	aod->blastType, "blat", aod->minIdentity);
axtBundleFreeList(&aod->bundleList);
}

// Assembly:
pushq %rbx
movq %rsi, %rcx
movq 0x8(%rdi), %rbx
movl 0x44(%rdi), %esi
movl 0x3c(%rdi), %edx
movq (%rbx), %rdi
movq 0x8(%rbx), %r8
movl 0x10(%rbx), %r9d
movsd 0x18(%rbx), %xmm0
movsd 0x28(%rbx), %xmm1
leaq 0x6bafd(%rip), %rax     # 0x7d3e1
pushq %rax
pushq 0x20(%rbx)
callq 0x1923c
popq %rax
popq %rcx
movq %rbx, %rdi
popq %rbx
jmp 0x17d9b
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/jkOwnLib/gfOut.c
// Function: gfOutputFree
void gfOutputFree(struct gfOutput **pOut)
/* Free up output */
{
struct gfOutput *out = *pOut;
if (out != NULL)
    {
    freeMem(out->data);
    freez(pOut);
    }
}

// Assembly:
movq (%rdi), %rax
testq %rax, %rax
je 0x11abd
pushq %rbx
movq %rdi, %rbx
movq 0x8(%rax), %rdi
callq 0x28c2d
movq %rbx, %rdi
popq %rbx
jmp 0x28c3d
retq
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/jkOwnLib/gfOut.c
// Function: axtMatchCount
static int axtMatchCount(struct axt *axt)
/* Return matches. */
{
int matchCount = 0;
int i;
for (i=0; i<axt->symCount; ++i)
    {
    if (axt->qSym[i] == axt->tSym[i])
        ++matchCount;
    }
return matchCount;
}

// Assembly:
movl 0x38(%rdi), %ecx
xorl %edx, %edx
testl %ecx, %ecx
cmovlel %edx, %ecx
xorl %eax, %eax
cmpq %rdx, %rcx
je 0x11aee
movq 0x40(%rdi), %rsi
movq 0x48(%rdi), %r8
movb (%rsi,%rdx), %sil
xorl %r9d, %r9d
cmpb (%r8,%rdx), %sil
sete %r9b
addl %r9d, %eax
incq %rdx
jmp 0x11aca
retq
nop
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/jkOwnLib/ooc.c
// Function: oocMaskCounts
void oocMaskCounts(char *oocFile, bits32 *tileCounts, int tileSize, bits32 maxPat)
/* Set items of tileCounts to maxPat if they are in oocFile. 
 * Effectively masks this out of index.*/
{
if (oocFile != NULL)
    {
    bits32 sig, psz;
    FILE *f = mustOpen(oocFile, "rb");
    boolean mustSwap = FALSE;

    mustReadOne(f, sig);
    mustReadOne(f, psz);
    if (sig == oocSig)
	mustSwap = FALSE;
    else if (sig == oocSigSwapped)
	{
	mustSwap = TRUE;
	psz = byteSwap32(psz);
	}
    else
        errAbort("Bad signature on %s\n", oocFile);
    if (psz != tileSize)
        errAbort("Oligo size mismatch in %s. Expecting %d got %d\n", 
            oocFile, tileSize, psz);
    if (mustSwap)
	{
	union {bits32 whole; UBYTE bytes[4];} u,v;
	while (readOne(f, u))
	    {
	    v.bytes[0] = u.bytes[3];
	    v.bytes[1] = u.bytes[2];
	    v.bytes[2] = u.bytes[1];
	    v.bytes[3] = u.bytes[0];
	    tileCounts[v.whole] = maxPat;
	    }
	}
    else
	{
	bits32 oli;
	while (readOne(f, oli))
	    tileCounts[oli] = maxPat;
	}
    fclose(f);
    }
}

// Assembly:
testq %rdi, %rdi
je 0x11c0a
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x18, %rsp
movl %ecx, %ebx
movq %rsi, %r14
movq %rdi, %r12
movl %edx, 0x10(%rsp)
leaq 0x6b8cc(%rip), %rsi     # 0x7d3e6
callq 0x1ec79
movq %rax, %r15
leaq 0x14(%rsp), %r13
pushq $0x4
popq %rbp
movq %rax, %rdi
movq %r13, %rsi
movq %rbp, %rdx
callq 0x1ed97
leaq 0xc(%rsp), %rsi
movq %r15, %rdi
movq %rbp, %rdx
callq 0x1ed97
movb $0x1, %bpl
movl (%r13), %eax
cmpl $0x584155f2, %eax       # imm = 0x584155F2
je 0x11b7f
cmpl $0xf2554158, %eax       # imm = 0xF2554158
jne 0x11b6e
movl 0xc(%rsp), %edi
callq 0x1f5a0
movl %eax, 0xc(%rsp)
xorl %ebp, %ebp
jmp 0x11b7f
leaq 0x6b874(%rip), %rdi     # 0x7d3e9
movq %r12, %rsi
xorl %eax, %eax
callq 0x223fb
movl 0xc(%rsp), %ecx
movl 0x10(%rsp), %edx
cmpl %edx, %ecx
je 0x11b9c
leaq 0x6b86c(%rip), %rdi     # 0x7d3fe
movq %r12, %rsi
xorl %eax, %eax
callq 0x223fb
leaq 0x8(%rsp), %r12
pushq $0x4
popq %r13
testb %bpl, %bpl
je 0x11bce
pushq $0x1
popq %rbp
movq %r12, %rdi
movq %r13, %rsi
movq %rbp, %rdx
movq %r15, %rcx
callq 0x6b20
cmpq $0x1, %rax
jne 0x11bf4
movl 0x8(%rsp), %eax
movl %ebx, (%r14,%rax,4)
jmp 0x11bad
pushq $0x1
popq %rbp
movq %r12, %rdi
movq %r13, %rsi
movq %rbp, %rdx
movq %r15, %rcx
callq 0x6b20
cmpq $0x1, %rax
jne 0x11bf4
movl 0x8(%rsp), %eax
bswapl %eax
movl %ebx, (%r14,%rax,4)
jmp 0x11bd1
movq %r15, %rdi
callq 0x66e0
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/jkOwnLib/ooc.c
// Function: oocMaskSimpleRepeats
void oocMaskSimpleRepeats(bits32 *tileCounts, int seedSize, bits32 maxPat)
/* Mask out simple repeats in index . */
{
int i, j, k;
int tileMask = (1<<(seedSize+seedSize))-1;
for (i=0; i<4; ++i)
    {
    for (j=0; j<4; ++j)
        {
        bits32 repeat = 0;
        for (k=0; k<8; ++k)
            {
            repeat <<= 2;
            repeat |= i;
            repeat <<= 2;
            repeat |= j;
            }
        repeat &= tileMask;
        tileCounts[repeat] = maxPat;
        }
    }
}

// Assembly:
leal (%rsi,%rsi), %ecx
pushq $-0x1
popq %rax
shll %cl, %eax
notl %eax
xorl %ecx, %ecx
pushq $0x8
popq %rsi
cmpl $0x4, %ecx
je 0x11c58
leal (,%rcx,4), %r8d
xorl %r9d, %r9d
cmpl $0x4, %r9d
je 0x11c54
xorl %r10d, %r10d
movl %esi, %r11d
subl $0x1, %r11d
jb 0x11c48
shll $0x4, %r10d
orl %r8d, %r10d
orl %r9d, %r10d
jmp 0x11c36
andl %eax, %r10d
movl %edx, (%rdi,%r10,4)
incl %r9d
jmp 0x11c2a
incl %ecx
jmp 0x11c1a
retq
nopl (%rax)
// File: /workspace/github_c_makefile_star2_O2/icebert[P]pblat/jkOwnLib/supStitch.c
// Function: ssFfItemFreeList
void ssFfItemFreeList(struct ssFfItem **pList)
/* Free a list of ssFfItems. */
{
struct ssFfItem *el, *next;
for (el = *pList; el != NULL; el = next)
    {
    next = el->next;
    ssFfItemFree(&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 0x11ca7
movq (%r15), %r15
movq %r14, %rdi
callq 0x11c5c
jmp 0x11c90
andq $0x0, (%rbx)
addq $0x10, %rsp
popq %rbx
popq %r14
popq %r15
retq