// bamtools_filter.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 10 December 2012
+// Last modified: 3 May 2013
// ---------------------------------------------------------------------------
// Filters BAM file(s) according to some user-specified criteria
// ***************************************************************************
const string ISREVERSESTRAND_PROPERTY = "isReverseStrand";
const string ISSECONDMATE_PROPERTY = "isSecondMate";
const string ISSINGLETON_PROPERTY = "isSingleton";
+const string LENGTH_PROPERTY = "length";
const string MAPQUALITY_PROPERTY = "mapQuality";
const string MATEPOSITION_PROPERTY = "matePosition";
const string MATEREFERENCE_PROPERTY = "mateReference";
const bool isSingleton = al.IsPaired() && al.IsMapped() && !al.IsMateMapped();
keepAlignment &= valueFilter.check(isSingleton);
}
+ else if ( propertyName == LENGTH_PROPERTY ) keepAlignment &= valueFilter.check(al.Length);
else if ( propertyName == MAPQUALITY_PROPERTY ) keepAlignment &= valueFilter.check(al.MapQuality);
else if ( propertyName == MATEPOSITION_PROPERTY ) keepAlignment &= ( al.IsPaired() && al.IsMateMapped() && valueFilter.check(al.MateRefID) );
else if ( propertyName == MATEREFERENCE_PROPERTY ) {
string tagFilterString = entireTagFilterString.substr(3);
// switch on tag type to set tag query value & parse filter token
+ int8_t asciiFilterValue, asciiQueryValue;
int32_t intFilterValue, intQueryValue;
uint32_t uintFilterValue, uintQueryValue;
float realFilterValue, realQueryValue;
bool keepAlignment = false;
switch (tagType) {
+ // ASCII tag type
+ case 'A':
+ if ( al.GetTag(tagName, asciiQueryValue) ) {
+ if ( FilterEngine<BamAlignmentChecker>::parseToken(tagFilterString, asciiFilterValue, compareType) ) {
+ tagFilter.Value = asciiFilterValue;
+ tagFilter.Type = compareType;
+ keepAlignment = tagFilter.check(asciiQueryValue);
+ }
+ }
+ break;
+
// signed int tag type
case 'c' :
case 's' :
break;
// string tag type
- case 'A':
+
case 'Z':
case 'H':
if ( al.GetTag(tagName, stringQueryValue) ) {
// flags
bool HasAlignmentFlagFilter;
bool HasInsertSizeFilter;
+ bool HasLengthFilter;
bool HasMapQualityFilter;
bool HasNameFilter;
bool HasQueryBasesFilter;
// filters
string AlignmentFlagFilter;
string InsertSizeFilter;
- string NameFilter;
+ string LengthFilter;
string MapQualityFilter;
+ string NameFilter;
string QueryBasesFilter;
string TagFilter; // support multiple ?
, OutputFilename(Options::StandardOut())
, HasAlignmentFlagFilter(false)
, HasInsertSizeFilter(false)
+ , HasLengthFilter(false)
, HasMapQualityFilter(false)
, HasNameFilter(false)
, HasQueryBasesFilter(false)
// int32_t conversion
else if ( propertyName == INSERTSIZE_PROPERTY ||
+ propertyName == LENGTH_PROPERTY ||
propertyName == MATEPOSITION_PROPERTY ||
propertyName == POSITION_PROPERTY
)
m_propertyNames.push_back(ISREVERSESTRAND_PROPERTY);
m_propertyNames.push_back(ISSECONDMATE_PROPERTY);
m_propertyNames.push_back(ISSINGLETON_PROPERTY);
+ m_propertyNames.push_back(LENGTH_PROPERTY);
m_propertyNames.push_back(MAPQUALITY_PROPERTY);
m_propertyNames.push_back(MATEPOSITION_PROPERTY);
m_propertyNames.push_back(MATEREFERENCE_PROPERTY);
if ( m_settings->HasIsReverseStrandFilter ) propertyTokens.insert( make_pair(ISREVERSESTRAND_PROPERTY, m_settings->IsReverseStrandFilter) );
if ( m_settings->HasIsSecondMateFilter ) propertyTokens.insert( make_pair(ISSECONDMATE_PROPERTY, m_settings->IsSecondMateFilter) );
if ( m_settings->HasIsSingletonFilter ) propertyTokens.insert( make_pair(ISSINGLETON_PROPERTY, m_settings->IsSingletonFilter) );
+ if ( m_settings->HasLengthFilter ) propertyTokens.insert( make_pair(LENGTH_PROPERTY, m_settings->LengthFilter) );
if ( m_settings->HasMapQualityFilter ) propertyTokens.insert( make_pair(MAPQUALITY_PROPERTY, m_settings->MapQualityFilter) );
if ( m_settings->HasNameFilter ) propertyTokens.insert( make_pair(NAME_PROPERTY, m_settings->NameFilter) );
if ( m_settings->HasQueryBasesFilter ) propertyTokens.insert( make_pair(QUERYBASES_PROPERTY, m_settings->QueryBasesFilter) );
const string flagDesc = "keep reads with this *exact* alignment flag (for more detailed queries, see below)";
const string insertDesc = "keep reads with insert size that matches pattern";
+ const string lengthDesc = "keep reads with length that matches pattern";
const string mapQualDesc = "keep reads with map quality that matches pattern";
const string nameDesc = "keep reads with name that matches pattern";
const string queryDesc = "keep reads with motif that matches pattern";
Options::AddValueOption("-alignmentFlag", "int", flagDesc, "", m_settings->HasAlignmentFlagFilter, m_settings->AlignmentFlagFilter, FilterOpts);
Options::AddValueOption("-insertSize", "int", insertDesc, "", m_settings->HasInsertSizeFilter, m_settings->InsertSizeFilter, FilterOpts);
+ Options::AddValueOption("-length", "int", lengthDesc, "", m_settings->HasLengthFilter, m_settings->LengthFilter, FilterOpts);
Options::AddValueOption("-mapQuality", "[0-255]", mapQualDesc, "", m_settings->HasMapQualityFilter, m_settings->MapQualityFilter, FilterOpts);
Options::AddValueOption("-name", "string", nameDesc, "", m_settings->HasNameFilter, m_settings->NameFilter, FilterOpts);
Options::AddValueOption("-queryBases", "string", queryDesc, "", m_settings->HasQueryBasesFilter, m_settings->QueryBasesFilter, FilterOpts);