static struct pfToken *fakeToken(struct pfToken *old,
enum pfTokType type, union pfTokVal *val)
/* Create a fake token. */
{
struct pfToken *tok = CloneVar(old);
tok->type = type;
tok->val = *val;
return tok;
}
static struct hashEl *hashElCloneList(struct hashEl *hels)
/* clone a list of hashEl objects */
{
struct hashEl *hels2 = NULL, *hel;
for (hel = hels; hel != NULL; hel = hel->next)
{
slSafeAddHead(&hels2, CloneVar(hel));
}
slReverse(&hels2);
return hels2;
}
struct dnaSeq *cloneDnaSeq(struct dnaSeq *orig)
/* Duplicate dna sequence in RAM. */
{
struct dnaSeq *seq = CloneVar(orig);
seq->name = cloneString(seq->name);
seq->dna = needHugeMem(seq->size+1);
memcpy(seq->dna, orig->dna, seq->size+1);
seq->mask = NULL;
if (orig->mask != NULL)
{
seq->mask = bitClone(orig->mask, seq->size);
}
return seq;
}
struct annoFilter *annoFilterCloneList(struct annoFilter *list)
/* Copy a list of annoFilters. */
{
struct annoFilter *newList = NULL, *oldF;
for (oldF = list; oldF != NULL; oldF = oldF->next)
{
struct annoFilter *newF = CloneVar(oldF);
newF->label = cloneString(oldF->label);
newF->values = cloneValues(oldF->values, oldF->type);
slAddHead(&newList, newF);
}
slReverse(&newList);
return newList;
}
struct psl *clonePsl(struct psl *psl)
/* Copy a psl to separate memory. */
{
struct psl *c = CloneVar(psl);
c->next = NULL;
c->qName = cloneString(psl->qName);
c->tName = cloneString(psl->tName);
AllocArray(c->blockSizes, c->blockCount);
CopyArray(psl->blockSizes, c->blockSizes, c->blockCount);
AllocArray(c->qStarts, c->blockCount);
CopyArray(psl->qStarts, c->qStarts, c->blockCount);
AllocArray(c->tStarts, c->blockCount);
CopyArray(psl->tStarts, c->tStarts, c->blockCount);
return c;
}
struct hashEl *hashElListHash(struct hash *hash)
/* Return a list of all elements of hash. Free return with hashElFreeList. */
{
int i;
struct hashEl *hel, *dupe, *list = NULL;
for (i=0; i<hash->size; ++i)
{
for (hel = hash->table[i]; hel != NULL; hel = hel->next)
{
dupe = CloneVar(hel);
slAddHead(&list, dupe);
}
}
return list;
}
void annoGratorGpVarSetFuncFilter(struct annoGrator *gSelf,
struct annoGratorGpVarFuncFilter *funcFilter)
/* If funcFilter is non-NULL, it specifies which functional categories
* to include in output; if NULL, by default intergenic variants are excluded and
* all other categories are included.
* NOTE: After calling this, call gpVar->setOverlapRule() because implementation
* of that depends on filter settings. */
{
struct annoGratorGpVar *self = (struct annoGratorGpVar *)gSelf;
freez(&self->funcFilter);
if (funcFilter != NULL)
self->funcFilter = CloneVar(funcFilter);
// Since our overlapRule behavior depends on filter settings, reevaluate:
aggvSetOverlapRule(gSelf, self->gpVarOverlapRule);
}
struct annoOption *annoOptionCloneList(struct annoOption *list)
/* Return a newly allocated copy of list. */
{
struct annoOption *newList = NULL, *afo;
for (afo = list; afo != NULL; afo = afo->next)
{
struct annoOption *newAfo = CloneVar(afo);
newAfo->spec.name = cloneString(afo->spec.name);
newAfo->value = NULL;
unsigned opFlags = opFlags;
if (opFlags & OPTION_MULTI)
{
switch (opFlags & OPTION_TYPE_MASK)
{
case OPTION_STRING:
newAfo->value = slNameCloneList((struct slName *)(afo->value));
break;
default:
errAbort("annoOptionCloneList: OPTION_MULTI implemented only for "
"OPTION_STRING (not 0x%x)", opFlags);
}
}
else
{
switch (opFlags & OPTION_TYPE_MASK)
{
// For numeric singleton values, we are overloading value.
case OPTION_DOUBLE:
case OPTION_FLOAT:
case OPTION_LONG_LONG:
case OPTION_INT:
case OPTION_BOOLEAN:
newAfo->value = afo->value;
break;
case OPTION_STRING:
newAfo->value = cloneString((char *)afo->value);
break;
default:
errAbort("annoOptionCloneList: unrecognized op type 0x%x", opFlags);
}
}
slAddHead(&newList, newAfo);
}
slReverse(&newList);
return newList;
}
struct microData *lookupGenes(struct sqlConnection *conn, char *table, struct microData *oldList)
/* Use gene list to lookup */
{
struct microData *newList = NULL, *gene, *geneCopy, *next;
struct hash *hash = newHash(0);
struct sqlResult *sr;
char **row;
char query[256];
/* Load up hash from lookup table. We are doing inverse lookup on it
* actually. */
sqlSafef(query, sizeof(query), "select name,value from %s", table);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
char *geneName = row[0];
char *expName = row[1];
hashAdd(hash, expName, cloneString(geneName));
}
/* Move genes in oldList that hit hash to newList.
* If more than one new gene hits then make a (shallow)
* dupe of it and put it on newList too. This would
* be a nightmare if we were actually going to free this
* memory, but as a simple file filter there's no need. */
for (gene = oldList; gene != NULL; gene = next)
{
struct hashEl *hel;
next = gene->next;
hel = hashLookup(hash, gene->name);
if (hel != NULL)
{
gene->name = hel->val;
slAddHead(&newList, gene);
while ((hel = hashLookupNext(hel)) != NULL)
{
geneCopy = CloneVar(gene);
geneCopy->name = hel->val;
slAddHead(&newList, geneCopy);
}
}
}
slReverse(&newList);
return newList;
}
int FASTCALL CompileVarBody(U16 flags, S16 *brackCnt, VAR *var, int *_elementsSize, int braceCnt, int cast)
{
int elementsSize, len;
S32 num;
VAR *childvar;
S16 braceCntStart;
int elementsStart;
elementsSize = *_elementsSize;
if(!PRECOMPILING) {
elementsStart = elementsSize;
}
if(comProc_LabelDeclaration(flags, brackCnt)) {
// catch the labels
if(braceCnt) {
if(GetNextWord()[0]=='}')
braceCnt--;
}
} else {
if(var->cast == VARCAST_STRUCT) {
braceCntStart = braceCnt;
if(szTemp[0]!='{') {
error(ERR_STRUCTELEMENTBRACE,szTemp);
} else {
GetNextWord();
braceCnt++;
}
childvar = FindFirstVariable(var->childVars);
while(childvar) {
braceCnt =
CompileVarBody(flags|CF_VARCHILD,brackCnt, childvar, &elementsSize, braceCnt, childvar->cast);
childvar = childvar->next;
if(childvar && !braceCnt) return 0;
}
if(braceCntStart != braceCnt) {
error(ERR_CLOSEBRACEEXP,var->label);
}
if(!PRECOMPILING)
var=var;
} else if(szTemp[0]=='{' && var->arraySize) {
int arsize = var->arraySize;
braceCntStart = braceCnt;
GetNextWord();
braceCnt++;
childvar = CloneVar(var, curVar, 0);
childvar->arraySize = 0;
do {
braceCnt =
CompileVarBody(flags|CF_VARCHILD,brackCnt, childvar, &elementsSize, braceCnt, childvar->cast);
arsize--;
} while(braceCnt && braceCnt > braceCntStart);
FreeVars(&childvar);
if(braceCntStart != braceCnt) {
error(ERR_CLOSEBRACEEXP,var->label);
}
if(!PRECOMPILING && arsize < 0) {
error(ERR_ARRAYTOOLARGE,var->label);
}
} else if(szTemp[0]=='"') {
if(varcasts[cast].size!=VARSIZE_BYTE)
error(ERR_STRINGNOTBYTE,var->label);
if(!DoString())
return 0;
if(!PRECOMPILING) {
len = lenSzStr;//(U16)strlen(szString);
if(var->arraySize && len > var->arraySize) {
len = var->arraySize;
szString[len?len-1:0] = '\0';
error(ERR_STRINGTOOLONG,szString);
}
BankWrite(szString,len);
if(var->arraySize) {
BankFill(0,var->arraySize-len);
elementsSize += var->arraySize;
} else {
elementsSize += len;
}
}
} else {
CompileImmediateInteger(0, &num, -4, 0);
if(!PRECOMPILING) {
if(strToInt_LabelObject) {
// do the fixup
AddFixOffs(
strToInt_LabelType,
(var->flags&VARFLAG_16BIT)?FIXOFFS_WORD:FIXOFFS_BYTE,
curBank->ptr,
0,
strToInt_LabelObject
);
}
if(var->flags&VARFLAG_16BIT) {
WriteCodeW(num);
elementsSize += 2;
} else {
WriteCodeB(num);
elementsSize ++;
}
}
}
if(braceCnt) {
if(GetNextWord()[0]=='}') {
braceCnt--;
} else if(szTemp[0]!=',') {
error(ERR_ARRAYCOMMAEXP,var->label);
} else {
if(GetNextWord()[0]=='}') {
braceCnt--;
}
}
}
}
if(!PRECOMPILING && (flags&CF_VARCHILD)) {
int amount = (elementsSize-elementsStart);
if(var->arraySize && amount < var->arraySize) {
BankFill(0,var->arraySize-amount);
elementsSize += var->arraySize-amount;
}
}
*_elementsSize = elementsSize;
return braceCnt;
}
double *cloneDouble(double x)
/* Return clone of double in dynamic memory */
{
return CloneVar(&x);
}
void reportCassette(struct altGraphX *ag, bool **em, int vs, int ve1, int ve2,
int altBpStart, int altBpEnd, int startV, int endV, FILE *out)
/* Write out both an altGraphX and two bed files. For a cassette exon the
edges are -
Name Vertexes Class
------ ---------- -----
exon1: startV->vs constitutive (cons 0)
junction1: vs->ve1 alternative1 (alt1 1)
exon2: ve1->altBpEnd alternative1 (alt1 1)
junction2: altBpEnd->ve2 alternative1 (alt1 1)
exon3: ve2->endV constitutive (cons 0)
junction3: vs->ve2 alternative2 (alt2 2)
*/
{
struct altGraphX *agLoc = NULL; /* Local altGraphX. */
struct evidence *ev = NULL, *evLoc = NULL;
int *vPos = ag->vPositions;
unsigned char *vT = ag->vTypes;
int *vPosLoc = NULL; /* Vertex Positions. */
int *eStartsLoc = NULL; /* Edge Starts. */
int *eEndsLoc = NULL; /* Edge ends. */
unsigned char *vTLoc = NULL; /* Vertex Types. */
int *eTLoc = NULL; /* Edge Types. */
int vCLoc = 0;
int eCLoc = 0;
int i =0;
struct dyString *dy = NULL;
if(out == NULL)
return;
AllocVar(agLoc);
agLoc->tName = cloneString(ag->tName);
agLoc->name = cloneString(ag->name);
agLoc->tStart = vPos[startV];
agLoc->tEnd = vPos[endV];
agLoc->strand[0] = ag->strand[0];
agLoc->vertexCount = vCLoc = 6;
agLoc->edgeCount = eCLoc = 6;
agLoc->id = altCassette;
/* Allocate some arrays. */
AllocArray(vPosLoc, vCLoc);
AllocArray(eStartsLoc, vCLoc);
AllocArray(eEndsLoc, vCLoc);
AllocArray(vTLoc, vCLoc);
AllocArray(eTLoc, vCLoc);
/* Fill in the vertex positions. */
vPosLoc[0] = vPos[startV];
vPosLoc[1] = vPos[vs];
vPosLoc[2] = vPos[ve1];
vPosLoc[3] = vPos[altBpEnd];
vPosLoc[4] = vPos[ve2];
vPosLoc[5] = vPos[endV];
/* Fill in the vertex types. */
vTLoc[0] = vT[startV];
vTLoc[1] = vT[vs];
vTLoc[2] = vT[ve1];
vTLoc[3] = vT[altBpEnd];
vTLoc[4] = vT[ve2];
vTLoc[5] = vT[endV];
/* Fill in the edges. */
/* Constitutive first exon. */
eStartsLoc[0] = 0;
eEndsLoc[0] = 1;
eTLoc[0] = 0;
ev = evidenceForEdge(ag, startV, vs);
evLoc = CloneVar(ev);
evLoc->mrnaIds = CloneArray(ev->mrnaIds, ev->evCount);
slAddHead(&agLoc->evidence, evLoc);
/* Exon inclusion junction. */
eStartsLoc[1] = 1;
eEndsLoc[1] = 2;
eTLoc[1] = 1;
ev = evidenceForEdge(ag, vs, ve1);
evLoc = CloneVar(ev);
evLoc->mrnaIds = CloneArray(ev->mrnaIds, ev->evCount);
slAddHead(&agLoc->evidence, evLoc);
/* Exon exclusion junction. */
eStartsLoc[2] = 1;
eEndsLoc[2] = 4;
eTLoc[2] = 2;
ev = evidenceForEdge(ag, vs, ve2);
evLoc = CloneVar(ev);
evLoc->mrnaIds = CloneArray(ev->mrnaIds, ev->evCount);
slAddHead(&agLoc->evidence, evLoc);
/* Cassette exon. */
eStartsLoc[3] = 2;
eEndsLoc[3] = 3;
eTLoc[3] = 1;
ev = evidenceForEdge(ag, ve1, altBpEnd);
evLoc = CloneVar(ev);
evLoc->mrnaIds = CloneArray(ev->mrnaIds, ev->evCount);
slAddHead(&agLoc->evidence, evLoc);
/* Exon inclusion junction. */
eStartsLoc[4] = 3;
eEndsLoc[4] = 4;
eTLoc[4] = 1;
ev = evidenceForEdge(ag, altBpEnd, ve2);
evLoc = CloneVar(ev);
evLoc->mrnaIds = CloneArray(ev->mrnaIds, ev->evCount);
slAddHead(&agLoc->evidence, evLoc);
/* Constitutive second exon. */
eStartsLoc[5] = 4;
eEndsLoc[5] = 5;
eTLoc[5] = 0;
ev = evidenceForEdge(ag, ve2, endV);
evLoc = CloneVar(ev);
evLoc->mrnaIds = CloneArray(ev->mrnaIds, ev->evCount);
slAddHead(&agLoc->evidence, evLoc);
slReverse(&agLoc->evidence);
dy = newDyString(ag->mrnaRefCount*36);
agLoc->mrnaRefCount = ag->mrnaRefCount;
for(i=0; i<ag->mrnaRefCount; i++)
dyStringPrintf(dy, "%s,", ag->mrnaRefs[i]);
sqlStringDynamicArray(dy->string, &agLoc->mrnaRefs, &i);
dyStringFree(&dy);
agLoc->mrnaTissues = CloneArray(ag->mrnaTissues, ag->mrnaRefCount);
agLoc->mrnaLibs = CloneArray(ag->mrnaLibs, ag->mrnaRefCount);
agLoc->vPositions = vPosLoc;
agLoc->edgeStarts = eStartsLoc;
agLoc->edgeEnds = eEndsLoc;
agLoc->vTypes = vTLoc;
agLoc->edgeTypes = eTLoc;
altGraphXTabOut(agLoc, out);
altGraphXFree(&agLoc);
}
void reportAlt3Prime(struct altGraphX *ag, bool **em, int vs, int ve1, int ve2,
int altBpStart, int altBpEnd, int startV, int endV, FILE *out)
/* Write out an altGraphX record for an alt3Prime splicing
event. Variable names are consistent with the rest of the program, but
can be misleading. Specifically vs = start of alt splicing, ve1 =
first end of alt splicing, etc. even though "vs" is really the end of
an exon. For an alt5Prime splice the edges are:
Name Vertexes Class
------ ---------- -----
exon1: startV->vs constituative (0)
junction1: vs->ve1 alternative (1)
junction2: vs->ve2 alternative (2)
exon2: ve1->e2 alternative (1)
exon3: ve2->endV constituative (0)
*/
{
struct altGraphX *agLoc = NULL; /* Local altGraphX. */
struct evidence *ev = NULL, *evLoc = NULL;
int *vPos = ag->vPositions;
unsigned char *vT = ag->vTypes;
int *vPosLoc = NULL; /* Vertex Positions. */
int *eStartsLoc = NULL; /* Edge Starts. */
int *eEndsLoc = NULL; /* Edge ends. */
unsigned char *vTLoc = NULL; /* Vertex Types. */
int *eTLoc = NULL; /* Edge Types. */
int vCLoc = 0;
int eCLoc = 0;
int edgeIx = 0, vertexIx = 0;
int i =0;
struct dyString *dy = NULL;
if(out == NULL)
return;
AllocVar(agLoc);
agLoc->tName = cloneString(ag->tName);
agLoc->name = cloneString(ag->name);
agLoc->tStart = vPos[startV];
agLoc->tEnd = vPos[endV];
agLoc->strand[0] = ag->strand[0];
agLoc->vertexCount = vCLoc = 6;
agLoc->edgeCount = eCLoc = 5;
agLoc->id = alt3Prime;
/* Allocate some arrays. */
AllocArray(vPosLoc, vCLoc);
AllocArray(eStartsLoc, eCLoc);
AllocArray(eEndsLoc, eCLoc);
AllocArray(vTLoc, vCLoc);
AllocArray(eTLoc, eCLoc);
/* Fill in the vertex positions. */
vertexIx = 0;
vPosLoc[vertexIx++] = vPos[startV]; /* 0 */
vPosLoc[vertexIx++] = vPos[vs]; /* 1 */
vPosLoc[vertexIx++] = vPos[ve1]; /* 2 */
vPosLoc[vertexIx++] = vPos[ve2]; /* 3 */
vPosLoc[vertexIx++] = vPos[ve2]; /* 4 */
vPosLoc[vertexIx++] = vPos[endV]; /* 5 */
/* Fill in the vertex types. */
vertexIx = 0;
vTLoc[vertexIx++] = vT[startV];
vTLoc[vertexIx++] = vT[vs];
vTLoc[vertexIx++] = vT[ve1];
vTLoc[vertexIx++] = vT[vs]; /* Faking a separate exon for the alt spliced portion. */
vTLoc[vertexIx++] = vT[ve2];
vTLoc[vertexIx++] = vT[endV];
edgeIx = 0;
/* Constitutive first exon. */
eStartsLoc[edgeIx] = 0;
eEndsLoc[edgeIx] = 1;
eTLoc[edgeIx] = 0;
ev = evidenceForEdge(ag, startV, vs);
evLoc = CloneVar(ev);
evLoc->mrnaIds = CloneArray(ev->mrnaIds, ev->evCount);
slAddHead(&agLoc->evidence, evLoc);
edgeIx++;
/* Alternative1 junction (shorter). */
eStartsLoc[edgeIx] = 1;
eEndsLoc[edgeIx] = 2;
eTLoc[edgeIx] = 1;
ev = evidenceForEdge(ag, vs, ve1);
evLoc = CloneVar(ev);
evLoc->mrnaIds = CloneArray(ev->mrnaIds, ev->evCount);
slAddHead(&agLoc->evidence, evLoc);
edgeIx++;
/* Alt2 junction (longer). */
eStartsLoc[edgeIx] = 1;
eEndsLoc[edgeIx] = 4;
eTLoc[edgeIx] = 2;
ev = evidenceForEdge(ag, vs, ve2);
evLoc = CloneVar(ev);
evLoc->mrnaIds = CloneArray(ev->mrnaIds, ev->evCount);
slAddHead(&agLoc->evidence, evLoc);
edgeIx++;
/* Alt1 portion of second exon. */
eStartsLoc[edgeIx] = 2;
eEndsLoc[edgeIx] = 3;
eTLoc[edgeIx] = 1;
ev = evidenceForEdge(ag, ve1, endV);
evLoc = CloneVar(ev);
evLoc->mrnaIds = CloneArray(ev->mrnaIds, ev->evCount);
slAddHead(&agLoc->evidence, evLoc);
edgeIx++;
/* Exon 2 constitutive (shorter exon) */
eStartsLoc[edgeIx] = 4;
eEndsLoc[edgeIx] = 5;
eTLoc[edgeIx] = 0;
ev = evidenceForEdge(ag, ve2, endV);
evLoc = CloneVar(ev);
evLoc->mrnaIds = CloneArray(ev->mrnaIds, ev->evCount);
slAddHead(&agLoc->evidence, evLoc);
edgeIx++;
/* Package up the evidence, tissues, etc. */
slReverse(&agLoc->evidence);
dy = newDyString(ag->mrnaRefCount*36);
agLoc->mrnaRefCount = ag->mrnaRefCount;
for(i=0; i<ag->mrnaRefCount; i++)
dyStringPrintf(dy, "%s,", ag->mrnaRefs[i]);
sqlStringDynamicArray(dy->string, &agLoc->mrnaRefs, &i);
dyStringFree(&dy);
agLoc->mrnaTissues = CloneArray(ag->mrnaTissues, ag->mrnaRefCount);
agLoc->mrnaLibs = CloneArray(ag->mrnaLibs, ag->mrnaRefCount);
agLoc->vPositions = vPosLoc;
agLoc->edgeStarts = eStartsLoc;
agLoc->edgeEnds = eEndsLoc;
agLoc->vTypes = vTLoc;
agLoc->edgeTypes = eTLoc;
altGraphXTabOut(agLoc, out);
altGraphXFree(&agLoc);
}
static struct linkedFeatures *cgapSageToLinkedFeatures(struct cgapSage *tag,
struct hash *libHash, struct hash *libTotHash, enum trackVisibility vis)
/* Convert a single CGAP tag to a list of linkedFeatures. */
{
struct linkedFeatures *libList = NULL;
struct linkedFeatures *skel = skeletonLf(tag);
int i;
if (vis == tvDense)
/* Just use the skeleton one. */
{
int tagTotal = 0;
int freqTotal = 0;
int libsUsed = 0;
for (i = 0; i < tag->numLibs; i++)
{
char libId[16];
char *libName;
safef(libId, sizeof(libId), "%d", tag->libIds[i]);
libName = hashMustFindVal(libHash, libId);
if (keepThisLib(libName, libId))
{
int libTotal = hashIntVal(libTotHash, libId);
tagTotal += libTotal;
freqTotal += tag->freqs[i];
libsUsed++;
}
}
if (libsUsed > 0)
{
skel->name = cloneString("whatever");
skel->score = (float)((double)freqTotal * (1000000/tagTotal));
skel->grayIx = grayIxForCgap(skel->score);
addSimpleFeature(skel);
libList = skel;
}
}
else if (vis == tvPack)
{
/* If it's pack mode, average tissues into one linkedFeature. */
struct hash *tpmHash = combineCgapSages(tag, libHash, libTotHash);
struct hashEl *tpmList = hashElListHash(tpmHash);
struct hashEl *tpmEl;
slSort(&tpmList, slNameCmp);
for (tpmEl = tpmList; tpmEl != NULL; tpmEl = tpmEl->next)
{
struct linkedFeatures *tiss = CloneVar(skel);
struct cgapSageTpmHashEl *tpm = (struct cgapSageTpmHashEl *)tpmEl->val;
char link[256];
char *encTissName = NULL;
double score = 0;
int len = strlen(tpmEl->name) + 32;
tiss->name = needMem(len);
safef(tiss->name, len, "%s (%d)", tpmEl->name, tpm->count);
encTissName = cgiEncode(tpmEl->name);
safef(link, sizeof(link), "i=%s&tiss=%s", tag->name, encTissName);
score = (double)tpm->freqTotal*(1000000/(double)tpm->libTotals);
tiss->score = (float)score;
tiss->grayIx = grayIxForCgap(score);
tiss->extra = cloneString(link);
freeMem(encTissName);
addSimpleFeature(tiss);
slAddHead(&libList, tiss);
}
hashElFreeList(&tpmList);
freeHashAndVals(&tpmHash);
}
else
/* full mode */
{
for (i = 0; i < tag->numLibs; i++)
{
char libId[16];
char *libName;
char link[256];
struct linkedFeatures *lf;
safef(libId, sizeof(libId), "%d", tag->libIds[i]);
libName = hashMustFindVal(libHash, libId);
if (keepThisLib(libName, libId))
{
lf = CloneVar(skel);
lf->name = cloneString(libName);
safef(link, sizeof(link), "i=%s&lib=%s", tag->name, libId);
lf->score = (float)tag->tagTpms[i];
lf->grayIx = grayIxForCgap(tag->tagTpms[i]);
lf->extra = cloneString(link);
addSimpleFeature(lf);
slAddHead(&libList, lf);
}
}
}
slSort(&libList, cgapLinkedFeaturesCmp);
slReverse(&libList);
return libList;
}
void chainSubsetOnQ(struct chain *chain, int subStart, int subEnd,
struct chain **retSubChain, struct chain **retChainToFree)
/* Get subchain of chain bounded by subStart-subEnd on
* query side. Return result in *retSubChain. In some
* cases this may be the original chain, in which case
* *retChainToFree is NULL. When done call chainFree on
* *retChainToFree. The score and id fields are not really
* properly filled in. */
{
struct chain *sub = NULL;
struct cBlock *oldB, *b, *bList = NULL;
int qStart = BIGNUM, qEnd = -BIGNUM;
int tStart = BIGNUM, tEnd = -BIGNUM;
/* Check for easy case. */
if (subStart <= chain->qStart && subEnd >= chain->qEnd)
{
*retSubChain = chain;
*retChainToFree = NULL;
return;
}
/* Build new block list and calculate bounds. */
for (oldB = chain->blockList; oldB != NULL; oldB = oldB->next)
{
if (oldB->qEnd <= subStart)
continue;
if (oldB->qStart >= subEnd)
break;
b = CloneVar(oldB);
if (b->qStart < subStart)
{
b->tStart += subStart - b->qStart;
b->qStart = subStart;
}
if (b->qEnd > subEnd)
{
b->tEnd -= b->qEnd - subEnd;
b->qEnd = subEnd;
}
slAddHead(&bList, b);
if (tStart > b->tStart)
tStart = b->tStart;
if (tEnd < b->tEnd)
tEnd = b->tEnd;
if (qStart > b->qStart)
qStart = b->qStart;
if (qEnd < b->qEnd)
qEnd = b->qEnd;
}
slReverse(&bList);
/* Make new chain based on old. */
if (bList != NULL)
{
AllocVar(sub);
sub->blockList = bList;
sub->qName = cloneString(chain->qName);
sub->qSize = chain->qSize;
sub->qStrand = chain->qStrand;
sub->qStart = qStart;
sub->qEnd = qEnd;
sub->tName = cloneString(chain->tName);
sub->tSize = chain->tSize;
sub->tStart = tStart;
sub->tEnd = tEnd;
sub->id = chain->id;
}
*retSubChain = *retChainToFree = sub;
}
void chainFastSubsetOnT(struct chain *chain, struct cBlock *firstBlock,
int subStart, int subEnd, struct chain **retSubChain, struct chain **retChainToFree)
/* Get subchain as in chainSubsetOnT. Pass in initial block that may
* be known from some index to speed things up. */
{
struct chain *sub = NULL;
struct cBlock *oldB, *b, *bList = NULL;
int qStart = BIGNUM, qEnd = -BIGNUM;
int tStart = BIGNUM, tEnd = -BIGNUM;
/* Check for easy case. */
if (subStart <= chain->tStart && subEnd >= chain->tEnd)
{
*retSubChain = chain;
*retChainToFree = NULL;
return;
}
/* Build new block list and calculate bounds. */
for (oldB = firstBlock; oldB != NULL; oldB = oldB->next)
{
if (oldB->tStart >= subEnd)
break;
b = CloneVar(oldB);
if (b->tStart < subStart)
{
b->qStart += subStart - b->tStart;
b->tStart = subStart;
}
if (b->tEnd > subEnd)
{
b->qEnd -= b->tEnd - subEnd;
b->tEnd = subEnd;
}
slAddHead(&bList, b);
if (qStart > b->qStart)
qStart = b->qStart;
if (qEnd < b->qEnd)
qEnd = b->qEnd;
if (tStart > b->tStart)
tStart = b->tStart;
if (tEnd < b->tEnd)
tEnd = b->tEnd;
}
slReverse(&bList);
/* Make new chain based on old. */
if (bList != NULL)
{
double sizeRatio;
AllocVar(sub);
sub->blockList = bList;
sub->qName = cloneString(chain->qName);
sub->qSize = chain->qSize;
sub->qStrand = chain->qStrand;
sub->qStart = qStart;
sub->qEnd = qEnd;
sub->tName = cloneString(chain->tName);
sub->tSize = chain->tSize;
sub->tStart = tStart;
sub->tEnd = tEnd;
sub->id = chain->id;
/* Fake new score. */
sizeRatio = (sub->tEnd - sub->tStart);
sizeRatio /= (chain->tEnd - chain->tStart);
sub->score = sizeRatio * chain->score;
}
*retSubChain = *retChainToFree = sub;
}