protected override bool ShouldSkipRead(BamAlignment alignment)
{
if (!alignment.IsMapped())
{
_statusCounter.AddDebugStatusCount("Skipped not mapped");
return(true);
}
if (alignment.IsSupplementaryAlignment())
{
_statusCounter.AddDebugStatusCount("Skipped supplementary");
return(true);
}
if (_filterForProperPairs && !alignment.IsProperPair())
{
_statusCounter.AddDebugStatusCount("Skipped improper pair");
return(true);
}
if (alignment.MapQuality < _minMapQuality)
{
_statusCounter.AddDebugStatusCount("Skipped low map quality");
return(true);
}
return(false);
}
protected override bool ShouldSkipRead(BamAlignment alignment)
{
if (!_filterPairLowMapQ && alignment.MapQuality > 0 && alignment.MapQuality < _minMapQuality)
{
_statusCounter.AddDebugStatusCount("Skipped read below mapQ");
return(true);
}
if (alignment.IsSupplementaryAlignment())
{
_statusCounter.AddDebugStatusCount("Skipped supplementary");
return(true);
}
if (alignment.IsSecondary())
{
_statusCounter.AddDebugStatusCount("Skipped secondary");
return(true);
}
if (_filterForProperPairs && !alignment.IsProperPair())
{
_statusCounter.AddDebugStatusCount("Skipped improper pair");
return(true);
}
return(false);
}