struct hash *buildMultiAlignHash()
/* Return a hash table filled with names of cDNAs that align more
* than once. */
{
FILE *aliFile;
struct cdaAli *cda;
struct hash *dupeHash;
char lastName[128];
char *name;
int dupeCount = 0;
lastName[0] = 0;
dupeHash = newHash(12);
aliFile = wormOpenGoodAli();
while (cda = cdaLoadOne(aliFile))
{
name = cda->name;
if (sameString(name, lastName))
{
if (!hashLookup(dupeHash, name))
{
hashAdd(dupeHash, name, NULL);
++dupeCount;
}
}
strcpy(lastName, name);
cdaFreeAli(cda);
}
fclose(aliFile);
printf("Found %d multiple alignments\n", dupeCount);
return dupeHash;
}
struct cdaAli *wormCdaAli(char *name)
/* Return named cDNA alignment or NULL if it doesn't exist. */
{
long offset;
wormOpenAliSnof();
if (!snofFindOffset(aliSnof, name, &offset))
return NULL;
fseek(aliFile, offset, SEEK_SET);
return cdaLoadOne(aliFile);
}
struct cdaAli *readAllCda()
/* Read in all worm Cda (cDNA alignments medium detail level) and return them. */
{
struct cdaAli *list = NULL, *el;
FILE *f = anyOpenGoodAli();
while ((el = cdaLoadOne(f)) != NULL)
{
// if (el->chromIx == 0 && el->chromStart < 1000000) /* uglyf */
slAddHead(&list, el);
}
slReverse(&list);
return list;
}
struct cdaAli *wormCdaAlisInRange(char *chromId, int start, int end)
/* Return list of cdna alignments that overlap range. */
{
struct cdaAli *list = NULL, *el;
char fileName[512];
FILE *ixFile, *aliFile;
bits32 sig;
int s, e;
long fpos;
aliFile = wormOpenGoodAli();
sprintf(fileName, "%s%s.alx", cdnaDir, chromId);
ixFile = mustOpen(fileName, "rb");
mustReadOne(ixFile, sig);
if (sig != alxSig)
errAbort("Bad signature on %s", fileName);
for (;;)
{
if (!readOne(ixFile, s))
break;
mustReadOne(ixFile, e);
mustReadOne(ixFile, fpos);
if (e <= start)
continue;
if (s >= end)
break;
AllocVar(el);
fseek(aliFile, fpos, SEEK_SET);
el = cdaLoadOne(aliFile);
if (el == NULL)
errAbort("Truncated cdnaAli file");
slAddHead(&list, el);
}
slReverse(&list);
fclose(aliFile);
fclose(ixFile);
return list;
}
