struct psl *nextPsl(struct lineFile *lf)
/* Read next line from file and convert it to psl. Return
* NULL at eof. */
{
char *line;
int lineSize;
char *words[32];
int wordCount;
if (!lineFileNext(lf, &line, &lineSize))
{
//warn("File %s appears to be incomplete\n", lf->fileName);
return NULL;
}
wordCount = chopTabs(line, words);
if (wordCount == 21)
{
return pslLoad(words);
}
else if (wordCount == 23)
{
return pslxLoad(words);
}
else
{
warn("Bad line %d of %s", lf->lineIx, lf->fileName);
return NULL;
}
}
static struct psl *queryNext(struct pslReader* pr)
/* read the next record from a query */
{
char **row = sqlNextRow(pr->sr);
if (row == NULL)
return NULL;
if (pr->isPslx)
return pslxLoad(row+pr->rowOffset);
else
return pslLoad(row+pr->rowOffset);
}
void pslReps(char *inName, char *bestAliName, char *repName)
/* Analyse inName and put best alignments for eacmRNA in estAliName.
* Put repeat info in repName. */
{
struct lineFile *in = pslFileOpen(inName);
FILE *bestFile = mustOpen(bestAliName, "w");
FILE *repFile = mustOpen(repName, "w");
int lineSize;
char *line;
char *words[32];
int wordCount;
struct psl *pslList = NULL, *psl = NULL;
char lastName[512];
int aliCount = 0;
quiet = sameString(bestAliName, "stdout") || sameString(repName, "stdout");
if (coverQSizeFile != NULL)
loadCoverQSizes(coverQSizeFile);
if (!quiet)
printf("Processing %s to %s and %s\n", inName, bestAliName, repName);
if (!noHead)
pslWriteHead(bestFile);
strcpy(lastName, "");
while (lineFileNext(in, &line, &lineSize))
{
if (((++aliCount & 0x1ffff) == 0) && !quiet)
{
printf(".");
fflush(stdout);
}
wordCount = chopTabs(line, words);
if (wordCount == 21)
psl = pslLoad(words);
else if (wordCount == 23)
psl = pslxLoad(words);
else
errAbort("Bad line %d of %s\n", in->lineIx, in->fileName);
if (!sameString(lastName, psl->qName))
{
doOneAcc(lastName, pslList, bestFile, repFile);
pslFreeList(&pslList);
safef(lastName, sizeof(lastName), "%s", psl->qName);
}
slAddHead(&pslList, psl);
}
doOneAcc(lastName, pslList, bestFile, repFile);
pslFreeList(&pslList);
lineFileClose(&in);
fclose(bestFile);
fclose(repFile);
if (!quiet)
printf("Processed %d alignments\n", aliCount);
}
static struct psl *fileNext(struct pslReader* pr)
/* read the next record from a file */
{
char *row[PSLX_NUM_COLS];
int numCols;
while ((numCols = lineFileChopNextTab(pr->lf, row, PSLX_NUM_COLS)) > 0)
{
lineFileExpectWords(pr->lf, (pr->isPslx ? PSLX_NUM_COLS : PSL_NUM_COLS), numCols);
if ((pr->chrom == NULL) || (sameString(row[13], pr->chrom)))
{
if (pr->isPslx)
return pslxLoad(row);
else
return pslLoad(row);
}
}
return NULL;
}
