struct composite *makeCompositeList(struct encode2Manifest *manList, struct hash *metaHash)
/* Return a list of composites with everything on manList */
{
struct composite *comp, *compList = NULL;
struct hash *compHash = hashNew(0);
char compName[256];
struct encode2Manifest *man;
for (man = manList; man != NULL; man = man->next)
{
char *realComp = tagVal(man, metaHash, "composite");
if (realComp != NULL)
safef(compName, sizeof(compName), "%s", realComp);
else
{
char *lab = emptyForNull(tagVal(man, metaHash, "lab"));
char *dataType = emptyForNull(tagVal(man, metaHash, "dataType"));
safef(compName, sizeof(compName), "comp%s%s", lab, dataType);
}
comp = hashFindVal(compHash, compName);
if (comp == NULL)
{
AllocVar(comp);
comp->name = cloneString(compName);
hashAdd(compHash, compName, comp);
slAddTail(&compList, comp);
}
struct slRef *manRef = slRefNew(man);
slAddTail(&comp->manRefList, manRef);
}
hashFree(&compHash);
return compList;
}
struct view *makeViewList(struct slRef *manRefList)
/* Return a list of views with everything on manList */
{
struct hash *hash = hashNew(0);
struct view *view, *viewList = NULL;
struct slRef *ref;
for (ref = manRefList; ref != NULL; ref = ref->next)
{
struct encode2Manifest *man = ref->val;
char *outputType = man->outputType;
char *format = man->format;
view = hashFindVal(hash, outputType);
if (view == NULL)
{
AllocVar(view);
view->name = cloneString(outputType);
view->format = cloneString(format);
char trackName[64];
safef(trackName, sizeof(trackName), "v%d", ++viewId);
view->trackName = cloneString(trackName);
hashAdd(hash, outputType, view);
slAddTail(&viewList, view);
}
if (!sameString(format, view->format))
errAbort("Multiple formats (%s and %s) in output_type %s",
format, view->format, view->name);
struct slRef *newRef = slRefNew(man);
slAddTail(&view->manRefList, newRef);
}
hashFree(&hash);
return viewList;
}
struct polygon *makeTriangle(int x, int y, int z)
/* Make triangle about center x,y,z */
{
struct polygon *tri;
struct point *pt;
int i;
AllocVar(tri);
tri->id = nextId();
tri->pointCount = 3;
AllocVar(pt);
strcpy(pt->acc, "acc1");
pt->pt.x = pt->x = x;
pt->pt.y = pt->y = y-100;
pt->z = z;
slAddTail(&tri->points, pt);
AllocVar(pt);
strcpy(pt->acc, "acc2");
pt->pt.x = pt->x = x-100;
pt->pt.y = pt->y = y+100;
pt->z = z;
slAddTail(&tri->points, pt);
AllocVar(pt);
strcpy(pt->acc, "acc3");
pt->pt.x = pt->x = x+100;
pt->pt.y = pt->y = y+100;
pt->z = z;
slAddTail(&tri->points, pt);
AllocArray(tri->persp, 3);
for (i=0, pt = tri->points; i < 3; ++i, pt = pt->next)
{
tri->persp[i].x = pt->x/2;
tri->persp[i].y = pt->y/2;
}
return tri;
}
static struct pipeline* pipelineNew(char ***cmds, unsigned options)
/* create a new pipeline object. Doesn't start processes */
{
static char *memPseudoCmd[] = {"[mem]", NULL};
struct pipeline *pl;
int iCmd;
AllocVar(pl);
pl->pipeFd = -1;
pl->options = options;
pl->procName = joinCmds(cmds);
if (cmds[0] == NULL)
errAbort("no commands in pipeline");
if (options & pipelineMemInput)
{
/* add proc for forked process to write memory to pipeline */
slAddTail(&pl->procs, plProcNew(memPseudoCmd, pl));
}
for(iCmd = 0; cmds[iCmd] != NULL; iCmd++)
slAddTail(&pl->procs, plProcNew(cmds[iCmd], pl));
return pl;
}
void cJoinX(char *j1, char *j2, char *j3)
/* cJoinX - Experiment in C joining.. */
{
struct joiner *joiner = joinerRead("../../makeDb/schema/all.joiner");
struct joinerDtf *a = joinerDtfFromDottedTriple(j1);
struct joinerDtf *b = joinerDtfFromDottedTriple(j2);
struct joinerDtf *c = joinerDtfFromDottedTriple(j3);
struct joinerPair *jpList = NULL, *jp;
struct joinerDtf *fieldList = NULL;
struct hash *visitedHash = hashNew(0);
slAddTail(&fieldList, a);
slAddTail(&fieldList, b);
slAddTail(&fieldList, c);
if (joinerDtfAllSameTable(fieldList))
printf("All in same table, easy enough!\n");
else
{
jpList = joinerFindRouteThroughAll(joiner, fieldList);
for (jp = jpList; jp != NULL; jp = jp->next)
{
printf("%s.%s.%s -> %s.%s.%s\n",
jp->a->database, jp->a->table, jp->a->field,
jp->b->database, jp->b->table, jp->b->field);
}
}
}
static struct gpFx *gpFxInExon(struct variant *variant, struct txCoords *txc, int exonIx,
struct genePred *pred, boolean predIsNmd,
struct dnaSeq *transcriptSeq, struct lm *lm)
/* Given a variant that overlaps an exon of pred, figure out what each allele does. */
{
struct gpFx *effectsList = NULL;
struct allele *allele = variant->alleles;
for ( ; allele ; allele = allele->next)
{
if (!allele->isReference)
{
if (pred->cdsStart != pred->cdsEnd)
{
// first find effects of allele in UTR, if any
effectsList = slCat(effectsList,
gpFxCheckUtr(allele, pred, txc, exonIx, predIsNmd, lm));
if (txc->startInCds >= 0)
effectsList = slCat(effectsList,
gpFxChangedCds(allele, pred, txc, exonIx, predIsNmd,
transcriptSeq, lm));
}
else
effectsList = slCat(effectsList,
gpFxChangedNoncodingExon(allele, pred, txc, exonIx, lm));
if (!predIsNmd)
{
// Was entire exon deleted?
int exonNumPos = exonIx;
if (pred->strand[0] == '-')
exonNumPos = pred->exonCount - 1 - exonIx;
uint exonStart = pred->exonStarts[exonNumPos], exonEnd = pred->exonEnds[exonNumPos];
if (variant->chromStart <= exonStart && variant->chromEnd >= exonEnd)
{
struct gpFx *effect = gpFxNew(allele->sequence, pred->name, exon_loss,
nonCodingExon, lm);
setNCExonVals(effect, exonIx, txc->startInCdna);
slAddTail(&effectsList, effect);
}
else
{
// If variant is in exon *but* within 3 bases of splice site,
// it also qualifies as splice_region_variant:
if ((variant->chromEnd > exonEnd-3 && variant->chromStart < exonEnd &&
exonIx < pred->exonCount - 1) ||
(variant->chromEnd > exonStart && variant->chromStart < exonStart+3 &&
exonIx > 0))
{
struct gpFx *effect = gpFxNew(allele->sequence, pred->name,
splice_region_variant, nonCodingExon, lm);
setNCExonVals(effect, exonIx, txc->startInCdna);
slAddTail(&effectsList, effect);
}
}
}
}
}
return effectsList;
}
void testPolyhOut()
{
struct polyhedron *ph;
AllocVar(ph);
ph->id = nextId();
ph->names[0] = cloneString("Jim");
ph->names[1] = cloneString("Kent");
ph->polygonCount = 2;
slAddTail(&ph->polygons, makeTriangle(0, 0, 0));
slAddTail(&ph->polygons, makeTriangle(0, 0, 100));
findBox(ph);
polyhedronCommaOut(ph, stdout);
printf("\n");
polyhedronFree(&ph);
}
static struct hash *htmlHeaderRead(char **pHtml, struct htmlCookie **pCookies)
/* Read in from second line through first blank line and
* save in hash. These lines are in the form name: value. */
{
struct hash *hash = hashNew(6);
for (;;)
{
char *line = htmlNextCrLfLine(pHtml);
char *word;
if (line == NULL)
{
warn("End of file in header");
break;
}
word = nextWord(&line);
if (word == NULL)
break;
line = skipLeadingSpaces(line);
hashAdd(hash, word, cloneString(line));
if (sameString(word, "Set-Cookie:"))
{
struct htmlCookie *cookie = parseCookie(line);
if (cookie != NULL)
slAddTail(pCookies, cookie);
}
}
return hash;
}
struct repBundle *bundleReplicates(struct replicate **pRepList)
/* Bundle together replicates, eating *pRepList in the process. */
{
struct replicate *rep, *nextRep;
struct repBundle *bundleList = NULL, *bundle;
struct dyString *hashName = dyStringNew(0);
struct hash *bundleHash = hashNew(0);
for (rep = *pRepList; rep != NULL; rep = nextRep)
{
nextRep = rep->next; // Going to clobber ->next field
dyStringClear(hashName);
struct slPair *tag;
for (tag = rep->tagList; tag != NULL; tag = tag->next)
{
if (!sameString(tag->name, "replicate") && !sameString(tag->name, "fileName"))
dyStringPrintf(hashName, "%s=%s;", tag->name, (char *)(tag->val));
}
bundle = hashFindVal(bundleHash, hashName->string);
if (bundle == NULL)
{
AllocVar(bundle);
slAddHead(&bundleList, bundle);
hashAddSaveName(bundleHash, hashName->string, bundle, &bundle->hashName);
}
slAddTail(&bundle->repList, rep);
}
slReverse(&bundleList);
*pRepList = NULL;
return bundleList;
}
struct consWiggle *wigMafWiggles(char *db, struct trackDb *tdb)
/* get conservation wiggle table names and labels from trackDb setting,
ignoring those where table doesn't exist */
{
char *fields[20];
int fieldCt;
int i;
char *wigTable, *wigLabel;
struct consWiggle *wig, *wigList = NULL;
char *setting = trackDbSetting(tdb, CONS_WIGGLE);
if (!setting)
return NULL;
fieldCt = chopLine(cloneString(setting), fields);
for (i = 0; i < fieldCt; i += 3)
{
wigTable = fields[i];
if (hTableExists(db, wigTable));
{
AllocVar(wig);
wig->table = cloneString(wigTable);
wigLabel = (i+1 == fieldCt ? DEFAULT_CONS_LABEL : fields[i+1]);
wig->leftLabel = cloneString(wigLabel);
wigLabel = (i+2 >= fieldCt ? wig->leftLabel : fields[i+2]);
wig->uiLabel = cloneString(wigLabel);
slAddTail(&wigList, wig);
}
}
return wigList;
}
/* make sure we have the whole range even if
* there isn't a maf loaded in this region
*/
static struct mafAli *padOutAli(struct mafAli *list, char *database,
char *chrom, int start, int end)
{
if (list == NULL)
{
struct mafAli *ali = getRefAli(database, chrom, start, end);
return ali;
}
int aliStart = list->components->start;
if (start != aliStart)
{
struct mafAli *ali = getRefAli(database, chrom, start, aliStart);
slAddHead(&list, ali);
}
struct mafAli *last = list;
for(; last->next; last = last->next)
;
int aliEnd = last->components->start + last->components->size;
if (end != aliEnd)
{
struct mafAli *ali = getRefAli(database, chrom, aliEnd, end);
slAddTail(&list, ali);
}
return list;
}
void addOutKeys(struct hash *tableHash, struct joinerPair *routeList,
struct tableJoiner **pTfList)
/* Add output keys to tableJoiners. These are in table hash.
* We may also have to add some fieldLess tables to the mix,
* which will get appended to *pTfList, and added to the hash
* if need be. */
{
struct joinerPair *route;
struct tableJoiner *tj;
char fullName[256];
for (route = routeList; route != NULL; route = route->next)
{
struct joinerDtf *a = route->a;
safef(fullName, sizeof(fullName), "%s.%s", a->database, a->table);
tj = hashFindVal(tableHash, fullName);
if (tj == NULL)
{
AllocVar(tj);
tj->database = a->database;
tj->table = a->table;
slAddTail(pTfList, tj);
hashAdd(tableHash, fullName, tj);
}
if (!inKeysOut(tj, route))
refAdd(&tj->keysOut, route);
}
}
static void addDtfListToBundle(struct hash *hash, struct tableJoiner **pList,
struct joinerDtf *dtfList, boolean addField)
/* Add table to hash/list if haven't seen it already. Optionally add
* field to table. */
{
char fullName[256];
struct joinerDtf *dtf, *dupe;
struct tableJoiner *tj;
for (dtf = dtfList; dtf != NULL; dtf = dtf->next)
{
safef(fullName, sizeof(fullName), "%s.%s", dtf->database, dtf->table);
tj = hashFindVal(hash, fullName);
if (tj == NULL)
{
AllocVar(tj);
hashAdd(hash, fullName, tj);
tj->database = dtf->database;
tj->table = dtf->table;
slAddHead(pList, tj);
}
if (addField)
{
dupe = joinerDtfClone(dtf);
slAddTail(&tj->fieldList, dupe);
}
}
}
static void jrRowExpand(struct joinedTables *joined,
struct joinedRow *jr, char **row,
int fieldOffset, int fieldCount, int keyOffset, int keyCount)
/* Add some more to row. */
{
int i;
struct slName **keys = jr->keys + keyOffset;
struct slName **fields = jr->fields + fieldOffset;
struct lm *lm = joined->lm;
struct slName *name;
if (fieldCount + fieldOffset > joined->fieldCount)
internalErr();
if (keyCount + keyOffset > joined->keyCount)
internalErr();
for (i=0; i<fieldCount; ++i)
{
name = lmSlName(lm, row[i]);
slAddTail(&fields[i], name);
}
row += fieldCount;
for (i=0; i<keyCount; ++i)
{
name = lmSlName(lm, row[i]);
slAddHead(&keys[i], name);
}
}
struct gdfGene *wormGetSomeGdfGeneList(char *baseName, int baseNameSize, struct wormGdfCache *cache)
/* Get all gdfGenes that start with a given name. */
{
int snIx;
int maxIx;
struct snof *snof;
FILE *f;
struct gdfGene *list = NULL, *el;
wormCacheSomeGdf(cache);
snof = cache->snof;
f = cache->file;
if (!snofFindFirstStartingWith(snof, baseName, baseNameSize, &snIx))
return NULL;
maxIx = snofElementCount(snof);
for (;snIx < maxIx; ++snIx)
{
long offset;
char *geneName;
snofNameOffsetAtIx(snof, snIx, &geneName, &offset);
if (strncmp(geneName, baseName, baseNameSize) != 0)
break;
fseek(f, offset, SEEK_SET);
el = gdfReadOneGene(f);
slAddTail(&list, el);
}
slReverse(&list);
return list;
}
static struct rqlParse *rqlParseOr(struct tokenizer *tkz)
/* Parse out and or or. */
{
struct rqlParse *p = rqlParseAnd(tkz);
struct rqlParse *parent = NULL;
for (;;)
{
char *tok = tokenizerNext(tkz);
if (tok == NULL || !sameString(tok, "or"))
{
tokenizerReuse(tkz);
return p;
}
else
{
if (parent == NULL)
{
p = rqlParseCoerce(p, rqlTypeBoolean);
AllocVar(parent);
parent->op = rqlOpOr;
parent->type = rqlTypeBoolean;
parent->children = p;
p = parent;
}
struct rqlParse *r = rqlParseCoerce(rqlParseAnd(tkz), rqlTypeBoolean);
slAddTail(&parent->children, r);
}
}
}
struct genScanGene *bundleGenes(struct genScanFeature *gsfList)
/* Bundle together features into genes. Cannibalizes gsfList. */
{
struct genScanFeature *gsf, *nextGsf;
struct genScanGene *geneList = NULL, *gene = NULL;
for (gsf = gsfList; gsf != NULL; gsf = nextGsf)
{
nextGsf = gsf->next;
if (gene == NULL || gene->id != gsf->geneId)
{
AllocVar(gene);
slAddHead(&geneList, gene);
gene->id = gsf->geneId;
gene->strand = gsf->strand;
gene->start = gsf->start;
gene->end = gsf->end;
}
slAddTail(&gene->featureList, gsf);
if (gsf->start < gene->start) gene->start = gsf->start;
if (gsf->end > gene->end) gene->end = gsf->end;
}
slReverse(&geneList);
return geneList;
}
void testPolyOut()
{
struct polygon *tri;
struct point *pt;
int i;
AllocVar(tri);
tri->id = 21060;
tri->pointCount = 4;
for (i=0; i<tri->pointCount; ++i)
{
AllocVar(pt);
sprintf(pt->acc, "point-%c", 'A'+i);
pt->x = 100 + i;
pt->y = 200 + i;
pt->z = 300 + i;
slAddTail(&tri->points, pt);
}
AllocArray(tri->persp,tri->pointCount);
for (i=0; i<tri->pointCount; ++i)
{
tri->persp[i].x = 50+i;
tri->persp[i].y = 100+i;
}
polygonCommaOut(tri, stdout);
printf("\n");
}
void setupTissueLibraryCache(struct sqlConnection *conn)
/* Hash all of the library and organism ids for this organism from
the mrna table. The key to the hash is the accession and the
value is a list of integers where the first is the library and
the second is the tissue. */
{
struct sqlResult *sr = NULL;
char query[256];
struct slInt *tissue = NULL, *library = NULL;
char **row = NULL;
int i = 0;
tissLibHash = newHash(12);
/* Now load up all of the accessions for this organism. */
for(i = 0; i < numDbTables; i++)
{
sqlSafef(query, sizeof(query), "select library, tissue, acc from %s inner join gbCdnaInfo on qName = acc",
dbTables[i]);
warn("%s", query);
sr = sqlGetResult(conn, query);
while((row = sqlNextRow(sr)) != NULL)
{
library = newSlInt(sqlSigned(row[0]));
tissue = newSlInt(sqlSigned(row[1]));
slAddTail(&library, tissue);
hashAdd(tissLibHash, row[2], library);
}
sqlFreeResult(&sr);
}
}
static struct gpFx *gpFxInIntron(struct variant *variant, struct txCoords *txc, int intronIx,
struct genePred *pred, boolean predIsNmd, char *altAllele,
struct lm *lm)
// Annotate a variant that overlaps an intron (and possibly splice region)
//#*** TODO: watch out for "introns" that are actually indels between tx seq and ref genome!
{
struct gpFx *effectsList = NULL;
boolean minusStrand = (pred->strand[0] == '-');
// If on - strand, flip intron number back to + strand for getting intron coords:
int intronPos = minusStrand ? (pred->exonCount - intronIx - 2) : intronIx;
int intronStart = pred->exonEnds[intronPos];
int intronEnd = pred->exonStarts[intronPos+1];
if (variant->chromEnd > intronStart && variant->chromStart < intronEnd)
{
enum soTerm soNumber = intron_variant;
if (variant->chromEnd > intronStart && variant->chromStart < intronStart+2)
// Within 2 bases of intron start(/end for '-'):
soNumber = minusStrand ? splice_acceptor_variant : splice_donor_variant;
if (variant->chromEnd > intronEnd-2 && variant->chromStart < intronEnd)
// Within 2 bases of intron end(/start for '-'):
soNumber = minusStrand ? splice_donor_variant : splice_acceptor_variant;
else if ((variant->chromEnd > intronStart+3 && variant->chromStart < intronStart+8) ||
(variant->chromEnd > intronEnd-8 && variant->chromStart < intronEnd+3))
// Within 3 to 8 bases of intron start or end:
soNumber = splice_region_variant;
if (predIsNmd)
// This transcript is already subject to nonsense-mediated decay, so the effect
// is probably not a big deal:
soNumber = NMD_transcript_variant;
struct gpFx *effects = gpFxNew(altAllele, pred->name, soNumber, intron, lm);
effects->details.intron.intronNumber = intronIx;
slAddTail(&effectsList, effects);
}
return effectsList;
}
void pushPosString(struct speciesInfo *si)
{
flushPosString(si);
struct slName *newName = newSlName(si->posString);
slAddTail(&si->posStrings, newName);
freez(&si->posString);
}
struct tagStanza *tagStanzaNewAtEnd(struct tagStorm *tagStorm, struct tagStanza *parent)
/* Create a new, empty stanza that is added as to head of child list of parent,
* or to tagStorm->forest if parent is NULL. */
/* Create new empty stanza that is added at tail of child list of parent */
{
struct tagStanza *stanza;
lmAllocVar(tagStorm->lm, stanza);
if (parent != NULL)
{
stanza->parent = parent;
slAddTail(&parent->children, stanza);
}
else
{
slAddTail(&tagStorm->forest, stanza);
}
return stanza;
}
void getAllSplices(char *database, FILE *f)
/* Write out table linking flybase genes with BDGP transcripts --
* unfortunately bdgpGeneInfo lacks -R* transcript/isoform identifiers,
* so strip those off of bdgpGene.name.
* This is not necessary with flyBaseGene/flyBase2004Xref where -R*'s
* are preserved.
*/
{
struct sqlConnection *conn = sqlConnect(database);
struct sqlResult *sr;
char query[256], **row;
struct geneAlt *altList = NULL, *alt;
struct hash *bdgpHash = newHash(16); /* Keyed by bdgp gene id. */
struct slName *n;
/* First build up list of all genes with flybase and bdgp ids. */
sqlSafef(query, sizeof(query), "select bdgpName,flyBaseId from bdgpGeneInfo");
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
AllocVar(alt);
alt->bdgpName = cloneString(row[0]);
alt->fbName = cloneString(row[1]);
slAddHead(&altList, alt);
hashAdd(bdgpHash, alt->bdgpName, alt);
}
sqlFreeResult(&sr);
slReverse(&altList);
/* Now associate splicing variants. */
sqlSafef(query, sizeof(query), "select name from %s", geneTable);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
char *s = row[0];
char *e = rStringIn("-R", s);
int size = e ? (e - s) : strlen(s);
char bdgpGene[16];
if (size >= sizeof(bdgpGene))
errAbort("'%s' too big", s);
memcpy(bdgpGene, s, size);
bdgpGene[size] = 0;
alt = hashMustFindVal(bdgpHash, bdgpGene);
n = slNameNew(s);
slAddTail(&alt->isoformList, n);
}
sqlFreeResult(&sr);
sqlDisconnect(&conn);
for (alt = altList; alt != NULL; alt = alt->next)
{
for (n = alt->isoformList; n != NULL; n = n->next)
fprintf(f, "%s\t%s\n", alt->fbName, n->name);
}
freeHash(&bdgpHash);
}
struct entity *addToEntityList(struct entity *entityList, struct cdaAli *ali)
/* If ali is non-null, make a new entity around it and add it to list. */
{
struct entity *entity;
if (ali == NULL)
return entityList;
entity = newEntity(ali);
slAddTail(&entityList, entity);
return entityList;
}
static void addTablesAccordingToTrackType(char *db, struct slName **pList, struct hash *uniqHash,
struct trackDb *track)
/* Parse out track->type and if necessary add some tables from it. */
{
struct slName *name;
char *trackDupe = cloneString(track->type);
if (trackDupe != NULL && trackDupe[0] != 0)
{
char *s = trackDupe;
char *type = nextWord(&s);
if (sameString(type, "wigMaf"))
{
static char *wigMafAssociates[] = {"frames", "summary"};
int i;
for (i=0; i<ArraySize(wigMafAssociates); ++i)
{
char *setting = wigMafAssociates[i];
char *table = trackDbSetting(track, setting);
if (table != NULL)
{
name = slNameNew(table);
slAddHead(pList, name);
hashAdd(uniqHash, table, NULL);
}
}
/* include conservation wiggle tables */
struct consWiggle *wig, *wiggles = wigMafWiggles(db, track);
slReverse(&wiggles);
for (wig = wiggles; wig != NULL; wig = wig->next)
{
name = slNameNew(wig->table);
slAddHead(pList, name);
hashAdd(uniqHash, wig->table, NULL);
}
}
if (track->subtracks)
{
struct slName *subList = NULL;
struct slRef *tdbRefList = trackDbListGetRefsToDescendantLeaves(track->subtracks);
slSort(&tdbRefList, trackDbRefCmp);
struct slRef *tdbRef;
for (tdbRef = tdbRefList; tdbRef != NULL; tdbRef = tdbRef->next)
{
struct trackDb *subTdb = tdbRef->val;
name = slNameNew(subTdb->table);
slAddTail(&subList, name);
hashAdd(uniqHash, subTdb->table, NULL);
}
pList = slCat(pList, subList);
}
}
freez(&trackDupe);
}
struct slPair *tagStanzaAppend(struct tagStorm *tagStorm, struct tagStanza *stanza,
char *tag, char *val)
/* Add tag with given value to stanza */
{
struct lm *lm = tagStorm->lm;
struct slPair *pair;
lmAllocVar(lm, pair);
pair->name = lmCloneString(lm, tag);
pair->val = lmCloneString(lm, val);
slAddTail(&stanza->tagList, pair);
return pair;
}
struct hash *hashPsls(char *pslFileName)
{
struct psl *pslList = NULL, *psl = NULL, *pslSubList = NULL, *pslNext = NULL;
struct hash *pslHash = newHash(15);
char *last = NULL;
char key[128];
char *tmp = NULL;
pslList = pslLoadAll(pslFileName);
/* Fix psl names */
for(psl = pslList; psl != NULL; psl = psl->next)
{
tmp = strrchr(psl->qName, ';');
*tmp = '\0';
tmp = strstr(psl->qName,prefix);
assert(tmp);
/* checks if there are 2 occurrences of ":" in probe name as in full name */
/* if probe name is shortened to fit in the seq table, there is only 1 ":"*/
/* e.g. full: consensus:HG-U133A:212933_x_at; short:HG-U133A:212933_x_at;*/
if (countChars(psl->qName, *prefix) == 2)
{
tmp = strstr(tmp+1,prefix);
assert(tmp);
}
tmp = tmp + strlen(prefix);
safef(psl->qName, strlen(psl->qName), "%s", tmp);
}
/* Sort based on query name. */
slSort(&pslList, pslCmpQuery);
/* For each psl, if it is has the same query name add it to the
sublist. Otherwise store the sublist in the hash and start
another. */
for(psl = pslList; psl != NULL; psl = pslNext)
{
pslNext = psl->next;
if(last != NULL && differentWord(last, psl->qName))
{
hashAddUnique(pslHash, last, pslSubList);
pslSubList = NULL;
}
slAddTail(&pslSubList, psl);
last = psl->qName;
}
/* Add the last sublist */
hashAddUnique(pslHash, last, pslSubList);
return pslHash;
}
void initPcm(struct ggcInfo *g, struct pcm *pcm, char *name, int pixels, bool detailed)
/* Allocate and initialize pcm */
{
ZeroVar(pcm);
pcm->name = cloneString(name);
pcm->pixels = pixels;
pcm->detailed = detailed;
AllocArray(pcm->match, pixels);
AllocArray(pcm->cover, pixels);
AllocArray(pcm->coverNondash, pixels);
AllocArray(pcm->count, pixels);
if (g != NULL)
slAddTail(&g->pcmList, pcm);
}
void addWigsInFile(char *fileName, struct bbiFile **pList)
/* Treate each non-empty non-sharp line of fileName as a bigWig file name
* and try to load the bigWig and add to list */
{
int i,count;
char **words, *buf = NULL;
readAllWords(fileName, &words ,&count, &buf);
for (i=0; i<count; ++i)
{
struct bbiFile *inFile = bigWigFileOpen(words[i]);
slAddTail(pList, inFile);
}
freeMem(words);
freeMem(buf);
}
struct raft *readRaftFile(char *fileName)
/* Read in a raft file. */
{
struct lineFile *lf = lineFileOpen(fileName, TRUE);
struct raft *raftList = NULL, *raft;
struct raftFrag *rf;
int lineSize, wordCount;
char *line, *words[16];
if (!lineFileNext(lf, &line, &lineSize))
errAbort("%s is empty", fileName);
if (!startsWith("ooGreedy version", line))
errAbort("%s isn't a raft file", fileName);
while (lineFileNext(lf, &line, &lineSize))
{
wordCount = chopLine(line, words);
if (wordCount == 0)
{
raft = NULL;
continue;
}
if (wordCount >= 9 && sameString(words[1], "raft"))
{
AllocVar(raft);
raft->name = cloneString(words[0]);
raft->baseCount = atoi(words[2]);
raft->fragCount = atoi(words[4]);
raft->defaultPos = atoi(words[6]);
slAddHead(&raftList, raft);
}
else if (wordCount == 4 || wordCount == 6)
{
AllocVar(rf);
rf->name = cloneString(words[2]);
rf->pos = atoi(words[0]);
rf->strand = words[1][0];
rf->size = atoi(words[3]);
rf->raft = raft;
slAddTail(&raft->rfList, rf);
}
else
errAbort("Bad line %d of %s", lf->lineIx, lf->fileName);
}
lineFileClose(&lf);
slReverse(&raftList);
return raftList;
}