void writeMousePartsAsMaf(FILE *f, struct hash *mouseHash,
char *ratMouseDir, char *mouseChrom,
int mouseStart, int mouseEnd, int mouseChromSize,
struct hash *rSizeHash, struct hash *dupeHash)
/* Write out mouse/rat alignments that intersect given region of mouse.
* This gets a little involved because we need to do random access on
* the mouse/rat alignment files, which are too big to fit into memory.
* On disk we have a mouse/rat alignment file for each mouse chromosome,
* and an index of it. When we first access a mouse chromosome we load
* the index for that chromosome into memory, and open the alignment file.
* We then do a seek and read to load a particular alignment. */
{
struct mouseChromCache *mcc = NULL;
struct binElement *list = NULL, *el;
char aliName[512];
/* Get cache for this mouse chromosome */
mcc = hashFindVal(mouseHash, mouseChrom);
if (mcc == NULL)
{
mcc = newMouseChromCache(mouseChrom, mouseChromSize, ratMouseDir);
hashAdd(mouseHash, mouseChrom, mcc);
}
if (mcc->lf == NULL)
return;
/* Get list of positions and process one axt into a maf for each */
list = binKeeperFindSorted(mcc->bk, mouseStart, mouseEnd);
for (el = list; el != NULL; el = el->next)
{
struct axt *axt;
struct mafAli temp;
long long *pPos, pos;
pPos = el->val;
pos = *pPos;
sprintf(aliName, "%s.%lld", mouseChrom, pos);
if (!hashLookup(dupeHash, aliName))
{
int rChromSize;
hashAdd(dupeHash, aliName, NULL);
lineFileSeek(mcc->lf, pos, SEEK_SET);
axt = axtRead(mcc->lf);
rChromSize = hashIntVal(rSizeHash, axt->qName);
prefixAxt(axt, rPrefix, mPrefix);
mafFromAxtTemp(axt, mouseChromSize, rChromSize, &temp);
mafWriteGood(f, &temp);
axtFree(&axt);
}
}
slFreeList(&list);
}
static void mafQueryOut(struct gfOutput *out, FILE *f)
/* Do axt oriented output - at end of processing query. */
{
struct axtData *aod = out->data;
struct axtBundle *gab;
for (gab = aod->bundleList; gab != NULL; gab = gab->next)
{
struct axt *axt;
for (axt = gab->axtList; axt != NULL; axt = axt->next)
{
struct mafAli temp;
mafFromAxtTemp(axt, gab->tSize, gab->qSize, &temp);
mafWrite(f, &temp);
}
}
axtBundleFreeList(&aod->bundleList);
}
void outputAxtAsMaf(FILE *f, struct axt *axt,
struct hash *tSizeHash, char *tPrefix, struct hash *qSizeHash, char *qPrefix)
/* Write out an axt in maf format. */
{
struct mafAli temp;
char *oldQ = axt->qName;
char *oldT = axt->tName;
char tName[256], qName[256];
snprintf(tName, sizeof(tName), "%s%s", tPrefix, axt->tName);
axt->tName = tName;
snprintf(qName, sizeof(qName), "%s%s", qPrefix, axt->qName);
axt->qName = qName;
mafFromAxtTemp(axt, hashIntVal(tSizeHash, oldT),
hashIntVal(qSizeHash, oldQ), &temp);
axt->qName = oldQ;
axt->tName = oldT;
mafWriteGood(f, &temp);
}