struct scaffold *readScaffoldsFromAgp(char *fileName)
/* Read in agp file and return as list of scaffolds. */
{
struct hash *scaffoldHash = newHash(17);
struct lineFile *lf = lineFileOpen(fileName, TRUE);
char *row[9];
int wordCount;
struct scaffold *scaffoldList = NULL, *scaffold;
struct agpFrag *frag;
int size;
for (;;)
{
wordCount = lineFileChop(lf, row);
if (wordCount <= 0)
break;
if (wordCount < 8)
lineFileShort(lf);
if (row[4][0] == 'N' || row[4][0] == 'U')
continue;
if (wordCount < 9)
lineFileShort(lf);
frag = agpFragLoad(row);
frag->chromStart -= 1;
frag->fragStart -= 1;
size = frag->fragEnd - frag->fragStart;
if (size != frag->chromEnd - frag->chromStart)
errAbort("scaffold/contig size mismatch line %d of %s", lf->lineIx, lf->fileName);
if (frag->strand[0] != '+')
errAbort("Strand not + line %d of %s", lf->lineIx, lf->fileName);
scaffold = hashFindVal(scaffoldHash, frag->chrom);
if (scaffold == NULL)
{
AllocVar(scaffold);
hashAdd(scaffoldHash, frag->chrom, scaffold);
slAddHead(&scaffoldList, scaffold);
}
slAddHead(&scaffold->list, frag);
if (frag->chromEnd > scaffold->size)
scaffold->size = frag->chromEnd;
}
slReverse(&scaffoldList);
for (scaffold = scaffoldList; scaffold != NULL; scaffold = scaffold->next)
slReverse(&scaffold->list);
printf("Got %d scaffolds in %s\n", slCount(scaffoldList), lf->fileName);
lineFileClose(&lf);
hashFree(&scaffoldHash);
return scaffoldList;
}
struct chrom *readChromScaffoldsFromAgp(char *fileName)
/* Read in agp file and return as list of chroms. */
{
struct hash *chromHash = newHash(17);
struct lineFile *lf = lineFileOpen(fileName, TRUE);
char *row[9];
int wordCount;
struct chrom *chromList = NULL, *chrom;
struct agpFrag *frag = NULL;
struct agpGap *gap = NULL;
char *chromName;
int chromSize = 0;
for (;;)
{
wordCount = lineFileChop(lf, row);
if (wordCount <= 0)
break;
if (wordCount < 8)
lineFileShort(lf);
if (row[4][0] == 'N' || row[4][0] == 'U')
{
/* need to get chromEnd from gaps to determine chrom size
* if the chrom ends with a gap */
gap = agpGapLoad(row);
chromName = gap->chrom;
chromSize = gap->chromEnd;
frag = NULL;
}
else
{
if (wordCount < 9)
lineFileShort(lf);
frag = agpFragLoad(row);
chromName = frag->chrom;
chromSize = frag->chromEnd;
frag->chromStart -= 1;
frag->fragStart -= 1;
if (frag->fragEnd - frag->fragStart !=
frag->chromEnd - frag->chromStart)
errAbort("chrom/scaffold size mismatch line %d of %s",
lf->lineIx, lf->fileName);
}
chrom = hashFindVal(chromHash, chromName);
if (chrom == NULL)
{
AllocVar(chrom);
slAddHead(&chromList, chrom);
hashAdd(chromHash, chromName, chrom);
}
chrom->size = max(chromSize, chrom->size);
if (frag != NULL)
slAddHead(&chrom->list, frag);
}
slReverse(&chromList);
for (chrom = chromList; chrom != NULL; chrom = chrom->next)
slReverse(&chrom->list);
verbose(1, "Got %d chroms in %s\n", slCount(chromList), lf->fileName);
lineFileClose(&lf);
hashFree(&chromHash);
return chromList;
}
