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 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);
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
int main (int argc, char* argv[])
{
QString pipelineFile("@DREAM3D_PIPELINE_FILE@");
// Instantiate the QCoreApplication that we need to get the current path and load plugins.
QCoreApplication app(argc, argv);
QCoreApplication::setOrganizationName("BlueQuartz Software");
QCoreApplication::setOrganizationDomain("bluequartz.net");
QCoreApplication::setApplicationName("PipelineRunnerTest");
// We need to change our working directory into the "DREAM3D_Data" directory because all the pipelines use relative paths
QDir dataDir = QDir(getDream3dDataDir());
#ifdef _MSC_VER
_chdir(dataDir.absolutePath().toLatin1().constData());
#else
chdir(dataDir.absolutePath().toLatin1().constData());
#endif
// Register all the filters including trying to load those from Plugins
FilterManager* fm = FilterManager::Instance();
DREAM3DPluginLoader::LoadPluginFilters(fm);
// Send progress messages from PipelineBuilder to this object for display
QMetaObjectUtilities::RegisterMetaTypes();
int err = 0;
// Read in the contents of the PipelineList file which contains all the Pipelines that we want
// to execute
QString contents;
{
// Read the Source File
QFileInfo fi(getPipelineListFile());
QFile source(getPipelineListFile());
source.open(QFile::ReadOnly);
contents = source.readAll();
source.close();
}
// Split the file into tokens using the newline character
QStringList list = contents.split(QRegExp("\\n"));
QStringListIterator sourceLines(list);
// Iterate over all the entries in the file and process each pipeline. Note that the order of the
// pipelines will probably matter
while (sourceLines.hasNext())
{
QString pipelineFile = sourceLines.next();
pipelineFile = pipelineFile.trimmed();
if(pipelineFile.isEmpty()) { continue; }
try
{
QFileInfo fi(pipelineFile);
pipelineFile = AdjustOutputDirectory(pipelineFile);
DREAM3D::unittest::CurrentMethod = fi.fileName().toStdString();
DREAM3D::unittest::numTests++;
ExecutePipeline(pipelineFile);
TestPassed(fi.fileName().toStdString());
DREAM3D::unittest::CurrentMethod = "";
}
catch (TestException& e)
{
TestFailed(DREAM3D::unittest::CurrentMethod);
std::cout << e.what() << std::endl;
err = EXIT_FAILURE;
}
}
return err;
}
