int ffCalcCdnaGapPenalty(int hGap, int nGap)
/* Return gap penalty for given h and n gaps. */
{
int acc = 2;
if (hGap > 400000) /* Discourage really long introns. */
{
acc += (hGap - 400000)/3000;
if (hGap > ffIntronMax)
acc += (hGap - ffIntronMax)/2000;
}
if (hGap < 0) /* Discourage jumping back in haystack. */
{
hGap = -8*hGap;
if (hGap > 48)
hGap = (hGap*hGap);
}
if (nGap < 0) /* Jumping back in needle gets rid of previous alignment. */
{
acc += -nGap;
nGap = 0;
}
acc += digitsBaseTwo(hGap)/2;
if (nGap != 0)
{
acc += digitsBaseTwo(nGap);
}
else
{
if (hGap > 30)
acc -= 1;
}
return acc;
}
struct hashEl *hashAddN(struct hash *hash, char *name, int nameSize, void *val)
/* Add name of given size to hash (no need to be zero terminated) */
{
struct hashEl *el;
if (hash->lm)
el = lmAlloc(hash->lm, sizeof(*el));
else
AllocVar(el);
el->hashVal = hashString(name);
int hashVal = el->hashVal & hash->mask;
if (hash->lm)
{
el->name = lmAlloc(hash->lm, nameSize+1);
memcpy(el->name, name, nameSize);
}
else
el->name = cloneStringZ(name, nameSize);
el->val = val;
el->next = hash->table[hashVal];
hash->table[hashVal] = el;
hash->elCount += 1;
if (hash->autoExpand && hash->elCount > (int)(hash->size * hash->expansionFactor))
{
/* double the size */
hashResize(hash, digitsBaseTwo(hash->size));
}
return el;
}
struct hash *hashSizedForTable(struct sqlConnection *conn, char *table)
/* Return a hash sized appropriately to hold all of table. */
{
char query[256];
int tableSize;
sqlSafef(query, sizeof(query), "select count(*) from %s", table);
tableSize = sqlQuickNum(conn, query);
printf("%s has %d rows\n", table, tableSize);
return newHash(digitsBaseTwo(tableSize) + 1);
}
struct hash *dnaSeqHash(struct dnaSeq *seqList)
/* Return hash of sequences keyed by name. */
{
int size = slCount(seqList)+1;
int sizeLog2 = digitsBaseTwo(size);
struct hash *hash = hashNew(sizeLog2);
struct dnaSeq *seq;
for (seq = seqList; seq != NULL; seq = seq->next)
hashAddUnique(hash, seq->name, seq);
return hash;
}
int gapPenalty(struct ffAli *left, struct ffAli *ali)
/* Calculate gap penalty using exon scoring. */
{
int nGap, hGap;
int minGap;
nGap = ali->nStart - left->nEnd;
assert(nGap >= 0);
hGap = ali->hStart - left->hStart;
if (hGap < 0)
{
hGap = 0;
nGap -= hGap;
}
minGap = (nGap < hGap ? nGap : hGap);
return (2 + digitsBaseTwo(hGap+minGap) + (nGap-minGap));
}
uint annoAssemblySeqSize(struct annoAssembly *aa, char *seqName)
/* Return the number of bases in seq which must be in aa's twoBitFile. */
{
if (aa->seqSizes == NULL)
aa->seqSizes = hashNew(digitsBaseTwo(aa->tbf->seqCount));
struct hashEl *hel = hashLookup(aa->seqSizes, seqName);
uint seqSize;
if (hel != NULL)
seqSize = (uint)(hel->val - NULL);
else
{
seqSize = (uint)twoBitSeqSize(aa->tbf, seqName);
char *pt = NULL;
hashAdd(aa->seqSizes, seqName, pt + seqSize);
}
return seqSize;
}
struct hash *hashKeyField(struct joinedTables *joined, int keyIx,
struct joinerField *jf)
/* Make a hash based on key field. */
{
int hashSize = digitsBaseTwo(joined->rowCount);
struct hash *hash = NULL;
struct joinedRow *jr;
if (hashSize > 20)
hashSize = 20;
hash = newHash(hashSize);
for (jr = joined->rowList; jr != NULL; jr = jr->next)
{
struct slName *key;
for (key = jr->keys[keyIx]; key != NULL; key = key->next)
{
if (jf->separator == NULL)
{
char *s = chopKey(jf->chopBefore, jf->chopAfter, key->name);
if (s[0] != 0)
hashAdd(hash, s, jr);
}
else
{
char *s = key->name, *e;
char sep = jf->separator[0];
while (s != NULL && s[0] != 0)
{
e = strchr(s, sep);
if (e != NULL)
*e++ = 0;
s = chopKey(jf->chopBefore, jf->chopAfter, s);
if (s[0] != 0)
hashAdd(hash, s, jr);
s = e;
}
}
}
}
return hash;
}
struct hash *readKeyHash(char *db, struct joiner *joiner,
struct joinerField *keyField, struct keyHitInfo **retList)
/* Read key-field into hash. Check for dupes if need be. */
{
struct sqlConnection *conn = sqlWarnConnect(db);
struct hash *keyHash = NULL;
struct keyHitInfo *khiList = NULL, *khi;
if (conn == NULL)
{
return NULL;
}
else
{
struct slName *table;
struct slName *tableList = getTablesForField(conn,keyField->splitPrefix,
keyField->table,
keyField->splitSuffix);
int rowCount = totalTableRows(conn, tableList);
int hashSize = digitsBaseTwo(rowCount)+1;
char query[256], **row;
struct sqlResult *sr;
int itemCount = 0;
int dupeCount = 0;
char *dupe = NULL;
if (rowCount > 0)
{
if (hashSize > hashMaxSize)
hashSize = hashMaxSize;
keyHash = hashNew(hashSize);
for (table = tableList; table != NULL; table = table->next)
{
safef(query, sizeof(query), "select %s from %s",
keyField->field, table->name);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
char *id = doChopsAndUpper(keyField, row[0]);
if (hashLookup(keyHash, id))
{
if (keyField->unique)
{
if (keyField->exclude == NULL ||
!slNameInList(keyField->exclude, id))
{
if (dupeCount == 0)
dupe = cloneString(id);
++dupeCount;
}
}
}
else
{
AllocVar(khi);
hashAddSaveName(keyHash, id, khi, &khi->name);
slAddHead(&khiList, khi);
++itemCount;
}
}
sqlFreeResult(&sr);
}
if (dupe != NULL)
{
warn("Error: %d duplicates in %s.%s.%s including '%s'",
dupeCount, db, keyField->table, keyField->field, dupe);
freez(&dupe);
}
verbose(2, " %s.%s.%s - %d unique identifiers\n",
db, keyField->table, keyField->field, itemCount);
}
slFreeList(&tableList);
}
sqlDisconnect(&conn);
*retList = khiList;
return keyHash;
}