static
void
runSAS(const SASOptions& opt)
{
static const float quantLevel[] = { 0.01f, 0.05f, 0.10f, 0.25f, 0.50f, 0.75f, 0.90f, 0.95f, 0.99f };
static const unsigned quantLevelCount(sizeof(quantLevel)/sizeof(float));
OutStream outs(opt.outputFilename);
std::ostream& report_os(outs.getStream());
ReadGroupStatsSet rgss;
rgss.load(opt.statsFilename.c_str());
const unsigned groupCount(rgss.size());
for (unsigned groupIndex(0); groupIndex<groupCount; ++groupIndex)
{
const ReadGroupStatsSet::KeyType& key(rgss.getKey(groupIndex));
#ifdef READ_GROUPS
report_os << "bamFile:\t" << key.bamLabel << '\n';
report_os << "readGroup:\t" << key.rgLabel << '\n';
#else
report_os << "group:\t" << key.bamLabel << '\n';
#endif
const ReadGroupStats& rgs(rgss.getStats(groupIndex));
report_os << "fragment length observations:\t" << rgs.fragStats.totalObservations() << '\n';
report_os << "fragment length quantiles:\n";
for (unsigned quantLevelIndex(0); quantLevelIndex<quantLevelCount; ++quantLevelIndex)
{
report_os << quantLevel[quantLevelIndex] << '\t' << rgs.fragStats.quantile(quantLevel[quantLevelIndex]) << '\n';
}
report_os << '\n';
}
}
static
void
mergeAlignmentStats(const MergeAlignmentStatsOptions& opt)
{
if (opt.statsFiles.empty())
{
log_os << "ERROR: No input files specified.\n";
exit(EXIT_FAILURE);
}
ReadGroupStatsSet all_rstats;
for (const std::string& file : opt.statsFiles)
{
ReadGroupStatsSet rstats;
rstats.load(file.c_str());
all_rstats.merge(rstats);
}
all_rstats.save(opt.outputFilename.c_str());
}