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 freePslOrXa(struct psl *psl, boolean isXa)
/* Free a psl that may be extended. */
{
if (isXa)
{
struct xAli *xa = (struct xAli *)psl;
xAliFree(&xa);
}
else
pslFree(&psl);
}
void xAliFreeList(struct xAli **pList)
/* Free a list of dynamically allocated xAli's */
{
struct xAli *el, *next;
for (el = *pList; el != NULL; el = next)
{
next = el->next;
xAliFree(&el);
}
*pList = NULL;
}
