void copyPslXaToTab(char *pslFile, char *tabFile)
/* copy a single PSL XA to the tab file */
{
struct xAli *xa;
char *row[23];
struct lineFile *lf = lineFileOpen(pslFile, TRUE);
struct pipeline *pl = NULL;
FILE *tabFh = NULL;
if (noSort)
tabFh = mustOpen(tabFile, "w");
else
{
if (pslCreateOpts & PSL_WITH_BIN)
pl = pipelineOpen(outPipeBin, pipelineWrite, tabFile, NULL);
else
pl = pipelineOpen(outPipeNoBin, pipelineWrite, tabFile, NULL);
tabFh = pipelineFile(pl);
}
while (lineFileRow(lf, row))
{
xa = xAliLoad(row);
if (pslCreateOpts & PSL_WITH_BIN)
fprintf(tabFh, "%u\t", hFindBin(xa->tStart, xa->tEnd));
xAliTabOut(xa, tabFh);
xAliFree(&xa);
}
lineFileClose(&lf);
if (noSort)
carefulClose(&tabFh);
else
{
pipelineWait(pl);
pipelineFree(&pl);
}
}
void copyPslToTab(char *pslFile, char *tabFile)
/* copy a single PSL to the tab file */
{
struct psl *psl;
struct lineFile *lf = pslFileOpen(pslFile);
struct pipeline *pl = NULL;
FILE *tabFh = NULL;
if (noSort)
tabFh = mustOpen(tabFile, "w");
else
{
if (pslCreateOpts & PSL_WITH_BIN)
pl = pipelineOpen(outPipeBin, pipelineWrite, tabFile, NULL);
else
pl = pipelineOpen(outPipeNoBin, pipelineWrite, tabFile, NULL);
tabFh = pipelineFile(pl);
}
while ((psl = pslNext(lf)) != NULL)
{
if (pslCreateOpts & PSL_WITH_BIN)
fprintf(tabFh, "%u\t", hFindBin(psl->tStart, psl->tEnd));
pslTabOut(psl, tabFh);
pslFree(&psl);
}
lineFileClose(&lf);
if (noSort)
carefulClose(&tabFh);
else
{
pipelineWait(pl);
pipelineFree(&pl);
}
}
void lineFileClose(struct lineFile **pLf)
/* Close up a line file. */
{
struct lineFile *lf;
if ((lf = *pLf) != NULL)
{
if (lf->pl != NULL)
{
pipelineWait(lf->pl);
pipelineFree(&lf->pl);
}
else if (lf->fd > 0 && lf->fd != fileno(stdin))
{
close(lf->fd);
freeMem(lf->buf);
}
#ifdef USE_TABIX
else if (lf->tabix != NULL)
{
if (lf->tabixIter != NULL)
ti_iter_destroy(lf->tabixIter);
ti_close(lf->tabix);
}
#endif // USE_TABIX
freeMem(lf->fileName);
metaDataFree(lf);
freez(pLf);
}
}
void textOutClose(struct pipeline **pCompressPipeline)
/* Flush and close stdout, wait for the pipeline to finish, and then free
* the pipeline object. */
{
if (pCompressPipeline && *pCompressPipeline)
{
fflush(stdout);
fclose(stdout);
pipelineWait(*pCompressPipeline);
pipelineFree(pCompressPipeline);
}
}
static void pslInputFree(struct pslInput **piPtr)
/* free pslInput object */
{
struct pslInput *pi = *piPtr;
if (pi != NULL)
{
assert(pi->pending == NULL);
pipelineWait(pi->pl);
pipelineFree(&pi->pl);
freez(piPtr);
}
}
void processFrameFiles(char *tabFile, int numFramesFiles, char **framesFiles)
/* combine and sort input files, adding bin column and write top tabFile */
{
/* sort by chrom location, accounting for bin column */
static char *cmd[] = {"sort", "-k", "2,2", "-k", "3,3n", NULL};
int i;
struct pipeline *pl = pipelineOpen1(cmd, pipelineWrite, tabFile, NULL);
FILE *sortFh = pipelineFile(pl);
for (i = 0; i < numFramesFiles; i++)
processFrameFile(sortFh, framesFiles[i]);
pipelineWait(pl);
}
void lineFileClose(struct lineFile **pLf)
/* Close up a line file. */
{
struct lineFile *lf;
if ((lf = *pLf) != NULL)
{
if (lf->pl != NULL)
{
pipelineWait(lf->pl);
pipelineFree(&lf->pl);
}
else if (lf->fd > 0 && lf->fd != fileno(stdin))
{
close(lf->fd);
freeMem(lf->buf);
}
freeMem(lf->fileName);
metaDataFree(lf);
freez(pLf);
}
}
