/* filters out all of psl with below a given percent */
struct psl *filterByBasePct(float percent, struct psl *pslList)
{
struct psl *psl=NULL, *ret=NULL;
int count=0, startCount=0, stopCount=0;
char buff[256];
startCount = slCount( pslList );
msg("filtering by seqId");
for(psl = pslList; psl != NULL; psl = psl->next)
{
float tmp = (float)(psl->match +psl->repMatch) / (psl->qSize - psl->nCount);
if(tmp >= percent)
{
struct psl *tmpPsl = copyPsl(psl);
slAddHead(&ret, tmpPsl);
}
/* let the user know we're making progress */
if(count % TICS == 0)
{
count = 0;
msg(".");
}
count++;
}
msg("\tDone.\n");
if(ret != NULL)
stopCount = slCount(ret);
sprintf(buff, "%d of %d had a basePct of %g or better.\n", stopCount, startCount, percent);
msg(buff);
slReverse(&ret);
return ret;
}
void outputAlignmentForStan(struct sqlConnection *conn, struct stanMad *sm, struct hash *iHash, FILE *out)
{
struct psl *pslList, *bestPsl = NULL;
char buff[1024];
int i;
struct imageClone *ic = NULL;
sprintf(buff, "%d", sm->clid);
printf("Looking for %s\n", buff);
ic = hashFindVal(iHash, buff);
if(ic != NULL)
{
/* first try looking for the image clones themselves... */
for(i=0; i<ic->numGenbank; i++)
{
char query[1024];
sqlSafef(query, sizeof query, "select * from all_est where qName='%s'", ic->genbankIds[i]);
pslList = pslLoadByQuery(conn, buff);
if(pslList != NULL)
{
slSort(&pslList, pslCmpScore);
if(bestPsl == NULL || (pslScore(pslList) > pslScore(bestPsl)))
pslFree(&bestPsl);
bestPsl = copyPsl(pslList);
}
pslFreeList(&pslList);
}
if(bestPsl != NULL)
{
freez(&bestPsl->qName);
sprintf(buff, "%d", sm->clid);
bestPsl->qName = cloneString(buff);
pslTabOut(bestPsl,out);
}
else
{
fprintf(out, "%d\talignment unknown\n", sm->clid);
}
}
else
{
fprintf(out, "%d\tunknown\n", sm->clid);
}
}
void copyPsls(struct gbSelect* select, unsigned pslFileType, FILE* outPslFh,
struct gbEntryCnts* counts)
/* Copy a PSL file from the work directory if it exists, count alignments
* for index. */
{
char inPsl[PATH_LEN];
struct lineFile* inPslLf;
struct psl* psl;
gbAlignedGetPath(select, gPslFileExt[pslFileType], gWorkDir, inPsl);
if (fileExists(inPsl))
{
gbVerbEnter(2, "installing from %s", inPsl);
inPslLf = gzLineFileOpen(inPsl);
while ((psl = pslNext(inPslLf)) != NULL)
{
copyPsl(select, pslFileType, psl, inPsl, outPslFh, counts);
pslFree(&psl);
}
gzLineFileClose(&inPslLf);
gbVerbLeave(2, "installing from %s", inPsl);
}
}
