void mafSummaryFreeList(struct mafSummary **pList)
/* Free a list of dynamically allocated mafSummary's */
{
struct mafSummary *el, *next;
for (el = *pList; el != NULL; el = next)
{
next = el->next;
mafSummaryFree(&el);
}
*pList = NULL;
}
long processMaf(struct mafAli *maf, struct hash *componentHash,
FILE *f, struct mafFile *mf, char *fileName)
/* Compute scores for each pairwise component in the maf and output to .tab file */
{
struct mafComp *mc = NULL, *nextMc = NULL;
struct mafSummary *ms, *msPending;
struct mafAli pairMaf;
long componentCount = 0;
struct mafComp *mcMaster = mafMaster(maf, mf, fileName);
struct mafComp *oldMasterNext = mcMaster->next;
char *e, *chrom;
char src[256];
strcpy(src, mcMaster->src);
chrom = chopPrefix(src);
for (mc = maf->components; mc != NULL; mc = nextMc)
{
nextMc = mc->next;
if (sameString(mcMaster->src, mc->src) || mc->size == 0)
continue;
/* create maf summary for this alignment component */
AllocVar(ms);
ms->chrom = cloneString(chrom);
/* both MAF and BED format define chromStart as 0-based */
ms->chromStart = mcMaster->start;
/* BED chromEnd is start+size */
ms->chromEnd = mcMaster->start + mcMaster->size;
ms->src = cloneString(mc->src);
/* remove trailing components (following initial .) to src name */
if ((e = strchr(ms->src, '.')) != NULL)
*e = 0;
/* construct pairwise maf for scoring */
ZeroVar(&pairMaf);
pairMaf.textSize = maf->textSize;
pairMaf.components = mcMaster;
mcMaster->next = mc;
mc->next = NULL;
ms->score = scorePairwise(&pairMaf);
ms->leftStatus[0] = mc->leftStatus;
ms->rightStatus[0] = mc->rightStatus;
/* restore component links to allow memory recovery */
mcMaster->next = oldMasterNext;
mc->next = nextMc;
/* output to .tab file, or save for merging with another block
* if this one is too small */
/* handle pending alignment block for this species, if any */
if ((msPending = (struct mafSummary *) hashFindVal(componentHash, ms->src)) != NULL)
{
/* there is a pending alignment block */
/* either merge it with the current block, or output it */
if (sameString(ms->chrom, msPending->chrom) &&
(ms->chromStart+1 - msPending->chromEnd < mergeGap))
{
/* merge pending block with current */
ms->score = mergeScores(msPending, ms);
ms->chromStart = msPending->chromStart;
ms->leftStatus[0] = msPending->leftStatus[0];
ms->rightStatus[0] = ms->rightStatus[0];
}
else
outputSummary(f, msPending);
hashRemove(componentHash, msPending->src);
mafSummaryFree(&msPending);
}
/* handle current alignment block (possibly merged) */
if (ms->chromEnd - ms->chromStart > minSize)
{
/* current block is big enough to output */
outputSummary(f, ms);
mafSummaryFree(&ms);
}
else
hashAdd(componentHash, ms->src, ms);
componentCount++;
}
return componentCount;
}
