static boolean validPsl(struct psl *psl)
/* check if a psl is internally consistent */
{
static FILE *devNull = NULL;
if (devNull == NULL)
devNull = mustOpen("/dev/null", "w");
return (pslCheck("", devNull, psl) == 0);
}
static void outputPsl(struct blastBlock *bb, unsigned flags, struct psl *psl,
FILE* pslFh, FILE* scoreFh)
/* output a psl and optional score */
{
pslTabOut(psl, pslFh);
if (scoreFh != NULL)
pslBuildScoresWrite(scoreFh, psl, bb->bitScore, bb->eVal);
pslCheck("blastToPsl", stderr, psl);
}
static void chkPsl(struct psl* psl, unsigned iRow, char* database,
char* table, struct metaDataTbls* metaDataTbls,
unsigned typeFlags)
/* Validate a PSL of a mrna/est to genome alignment against the metadata.
* Also count the number of alignments of a mrna. */
{
unsigned chromSize = getChromSize(database, psl->tName);
struct metaData* md = metaDataTblsFind(metaDataTbls, psl->qName);
char pslDesc[128];
if (gbVerbose >= 3)
gbVerbMsg(3, "chkPsl %s:%d %s %s", table, iRow, psl->qName, psl->tName);
safef(pslDesc, sizeof(pslDesc), "psl %s.%s row %u", database, table, iRow);
/* check that we have sequence info and compare sizes sizes */
if (chromSize == 0)
gbError("%s: tName not a valid chromosome: \"%s\"", pslDesc, psl->tName);
else
if (chromSize != psl->tSize)
gbError("%s: tSize %u != chromosome %s size %u",
pslDesc, psl->tSize, psl->tName, chromSize);
if (md == NULL)
gbError("%s: qName not in mrna table as type %s: \"%s\"",
pslDesc, gbFmtSelect(typeFlags & GB_TYPE_MASK), psl->qName);
else if (md->inSeq)
{
if (!md->inGbIndex)
gbError("%s: qName not in gbIndex as type %s: \"%s\""
" (Note: this can be caused by GenBank entries that were changed from type mRNA to other RNA types)", pslDesc,
gbFmtSelect(typeFlags & GB_TYPE_MASK), psl->qName);
else
{
if (typeFlags != md->typeFlags)
gbError("%s: alignment for %s type %s doesn't match expected %s",
pslDesc, psl->qName, gbFmtSelect(md->typeFlags),
gbFmtSelect(typeFlags));
}
if (md->seqSize != psl->qSize)
gbError("%s: qSize %u != %s size %u",
pslDesc, psl->qSize, psl->qName, md->seqSize);
md->numAligns++;
}
/* validate consistency of PSL */
if (pslCheck(pslDesc, stderr, psl))
errorCnt++;
}
static void outputPsl(struct psl *psl, FILE* pslFh)
/* output a psl */
{
pslTabOut(psl, pslFh);
pslCheck("blastXmlToPsl", stderr, psl);
}
