ContextMap::ContextMap()
{
// map requires sorted input
setSortedInput(true);
setLeftJoin(true);
setColumnOpsMethods(true);
}
ContextMerge::ContextMerge()
{
setSortedInput(true);
setUseMergedIntervals(true);
setColumnOpsMethods(true);
setExplicitBedOutput(true);
//merge has no default columnOps the way map does, so we'll need to clear those.
_keyListOps->setColumns("");
_keyListOps->setOperations("");
}
ContextMap::ContextMap()
{
// map requires sorted input
setSortedInput(true);
setLeftJoin(true);
// default to BED score column
setColumn(5);
// default to "sum"
setColumnOperation("sum");
// default to "." as a NULL value
setNullValue('.');
}
ContextGroupBy::ContextGroupBy()
: _printFullCols(false),
_ignoreCase(false)
{
setSortedInput(true);
_noEnforceCoordSort = true;
setColumnOpsMethods(true);
setExplicitBedOutput(true);
//For columnOps, groupBy has default operation sum but no default column,
///so we have to clear that.
//
_keyListOps->setColumns("");
}
ContextClosest::ContextClosest()
: _haveTieMode(false),
_ignoreOverlaps(false),
_ignoreUpstream(false),
_ignoreDownstream(false),
_reportDistance(false),
_signDistance(false),
_haveStrandedDistMode(false),
_diffNames(false),
_tieMode(ALL_TIES),
_strandedDistMode(REF_DIST),
_multiDbMode(EACH_DB)
{
// closest requires sorted input
setSortedInput(true);
}
bool ContextBase::handle_sorted()
{
setSortedInput(true);
markUsed(_i - _skipFirstArgs);
return true;
}
ContextFisher::ContextFisher() {
setSortedInput(true);
setUseMergedIntervals(false);
}
