static void printRetroAlignments(struct psl *pslList, int startFirst, char *hgcCommand,
char *aliTable, char *itemIn)
/* Print list of mRNA alignments. */
{
if (pslList == NULL || aliTable == NULL)
return;
printAlignmentsSimple(pslList, startFirst, hgcCommand, aliTable, itemIn);
#ifdef UNUSED /* Does nothing in face in the end except trim the psls that nobody looks at. */
struct psl *psl = pslList;
for (psl = pslList; psl != NULL; psl = psl->next)
{
if ( pslTrimToTargetRange(psl, winStart, winEnd) != NULL
&&
!startsWith("xeno", aliTable)
&& !(startsWith("user", aliTable) && pslIsProtein(psl))
&& psl->tStart == startFirst
)
{
char otherString[512];
safef(otherString, sizeof(otherString), "%d&aliTable=%s",
psl->tStart, aliTable);
}
}
#endif /* DOES_NOTHING */
}
void oneChrom(char *database, char *chrom, char *refAliTrack, char *bedTrack,
struct hash *otherHash, struct stats *stats)
/* Process one chromosome. */
{
struct bed *bedList = NULL, *bed;
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr;
char **row;
int rowOffset;
int chromSize = hChromSize(database, chrom);
struct binKeeper *bk = binKeeperNew(0, chromSize);
struct psl *pslList = NULL;
struct dnaSeq *chromSeq = NULL;
if (endsWith(bedTrack, ".bed"))
{
struct lineFile *lf = lineFileOpen(bedTrack, TRUE);
char *row[3];
while (lineFileRow(lf, row))
{
if (sameString(chrom, row[0]))
{
bed = bedLoad3(row);
slAddHead(&bedList, bed);
}
}
lineFileClose(&lf);
}
else
{
sr = hChromQuery(conn, bedTrack, chrom, NULL, &rowOffset);
while ((row = sqlNextRow(sr)) != NULL)
{
bed = bedLoad3(row+rowOffset);
slAddHead(&bedList, bed);
}
sqlFreeResult(&sr);
}
slReverse(&bedList);
uglyf("Loaded beds\n");
sr = hChromQuery(conn, refAliTrack, chrom, NULL, &rowOffset);
while ((row = sqlNextRow(sr)) != NULL)
{
struct psl *psl = pslLoad(row + rowOffset);
slAddHead(&pslList, psl);
binKeeperAdd(bk, psl->tStart, psl->tEnd, psl);
}
sqlFreeResult(&sr);
uglyf("Loaded psls\n");
chromSeq = hLoadChrom(database, chrom);
/* Fetch entire chromosome into memory. */
uglyf("Loaded human seq\n");
for (bed = bedList; bed != NULL; bed = bed->next)
{
struct binElement *el, *list = binKeeperFind(bk, bed->chromStart, bed->chromEnd);
for (el = list; el != NULL; el = el->next)
{
struct psl *fullPsl = el->val;
struct psl *psl = pslTrimToTargetRange(fullPsl,
bed->chromStart, bed->chromEnd);
if (psl != NULL)
{
foldPslIntoStats(psl, chromSeq, otherHash, stats);
pslFree(&psl);
}
}
slFreeList(&list);
stats->bedCount += 1;
stats->bedBaseCount += bed->chromEnd - bed->chromStart;
sqlFreeResult(&sr);
}
freeDnaSeq(&chromSeq);
pslFreeList(&pslList);
binKeeperFree(&bk);
hFreeConn(&conn);
}
