void chimpSuperQuals(char *agpFile, char *qacInName, char *qacOutName)
/* chimpSuperQuals - Map chimp quality scores from contig to supercontig.. */
{
struct hash *qacHash = qacReadToHash(qacInName);
struct scaffold *scaffold, *scaffoldList = readScaffoldsFromAgp(agpFile);
FILE *f = mustOpen(qacOutName, "w");
struct qaSeq qa;
struct agpFrag *frag;
struct qac *qac;
int bufSize = 0;
UBYTE *buf = NULL;
int qaMaxSize = 0;
int fragSize;
int count = 0;
qacWriteHead(f);
ZeroVar(&qa);
for (scaffold = scaffoldList; scaffold != NULL; scaffold = scaffold->next)
{
/* Set up qa to hold uncompressed quals for whole scaffold. */
qa.name = scaffold->list->chrom;
qa.size = scaffold->size;
if (qaMaxSize < qa.size)
{
freez(&qa.qa);
qa.qa = needHugeZeroedMem(qa.size);
qaMaxSize = qa.size;
}
/* Uncompress contig quality scores and copy into scaffold's quality buffer. */
for (frag = scaffold->list; frag != NULL; frag = frag->next)
{
qac = hashMustFindVal(qacHash, frag->frag);
if (bufSize < qac->uncSize)
{
freez(&buf);
bufSize = qac->uncSize;
buf = needMem(bufSize);
}
rleUncompress(qac->data, qac->compSize, buf, qac->uncSize);
fragSize = frag->fragEnd - frag->fragStart;
memcpy(qa.qa + frag->chromStart, buf + frag->fragStart, fragSize);
}
/* Compress and write it out. */
qacWriteNext(f, &qa);
++count;
}
carefulClose(&f);
}
void chimpHiQualDiffs(char *axtDir, char *qacName, char *bedName)
/* chimpHiQualDiffs - Create list of chimp high quality differences. */
{
struct hash *qacHash = qacReadToHash(qacName);
struct fileInfo *axtEl, *axtList = listDirX(axtDir, "*.axt", TRUE);
FILE *f = mustOpen(bedName, "w");
if (axtList==NULL)
axtList = listDirX(axtDir, "*.axt.gz", TRUE);
if (axtList==NULL)
printf("No axt files were found in the '%s' directory.\n",axtDir);
for (axtEl = axtList; axtEl != NULL; axtEl = axtEl->next)
axtHiQualDiffs(axtEl->name, qacHash, f);
carefulClose(&f);
}
void qacAgpLift(char *agpFile, char *qacInName, char *qacOutName)
/* qacAgpLift - Use AGP to combine per-scaffold qac into per-chrom qac. */
{
struct hash *qacHash = qacReadToHash(qacInName);
struct chrom *chrom, *chromList = readChromScaffoldsFromAgp(agpFile);
FILE *f = mustOpen(qacOutName, "w");
struct qaSeq qa;
struct agpFrag *frag;
struct qac *qac;
int bufSize = 0;
UBYTE *buf = NULL;
int qaMaxSize = 0;
int fragSize;
int count = 0;
qacWriteHead(f);
ZeroVar(&qa);
for (chrom = chromList; chrom != NULL; chrom = chrom->next)
{
/* Set up qa to hold uncompressed quals for whole chrom. */
qa.name = chrom->list->chrom;
verbose(1, " %s size=%d\n", chrom->list->chrom, chrom->size);
qa.size = chrom->size;
if (qaMaxSize < qa.size)
{
qa.qa = needHugeZeroedMem(qa.size);
qaMaxSize = qa.size;
}
else
{
zeroBytes(qa.qa, qa.size);
}
/* Uncompress contig quality scores and copy into chrom's quality buffer. */
for (frag = chrom->list; frag != NULL; frag = frag->next)
{
struct hashEl *hel;
fragSize = frag->fragEnd - frag->fragStart;
if ((hel = hashLookup(qacHash, frag->frag)) != NULL)
{
qac = (struct qac *) hel->val;
if (bufSize < qac->uncSize)
{
freez(&buf);
bufSize = qac->uncSize;
buf = needMem(bufSize);
}
rleUncompress(qac->data, qac->compSize, buf, qac->uncSize);
if (frag->strand[0] == '-')
reverseBytes((char*)buf, qac->uncSize);
memcpy(qa.qa + frag->chromStart, buf + frag->fragStart, fragSize);
}
else
{
/* agp frag not found in qac hash -- missing data */
if (mScore < 0)
errAbort("missing data: no quality scores for %s", frag->frag);
/* fill in missing data with specified score */
memset(qa.qa + frag->chromStart, mScore, fragSize);
}
}
/* Compress and write it out. */
qacWriteNext(f, &qa);
++count;
}
carefulClose(&f);
}
