const PropertyFilterValue& valueFilter = (*propertyIter).second;
if ( propertyName == ALIGNMENTFLAG_PROPERTY ) keepAlignment &= valueFilter.check(al.AlignmentFlag);
- else if ( propertyName == CIGAR_PROPERTY ) {
+ else if ( propertyName == CIGAR_PROPERTY ) {
stringstream cigarSs;
const vector<CigarOp>& cigarData = al.CigarData;
if ( !cigarData.empty() ) {
bool checkAlignmentTag(const PropertyFilterValue& valueFilter, const BamAlignment& al) {
- // ensure filter contains string data
- Variant entireTagFilter = valueFilter.Value;
- if ( !entireTagFilter.is_type<string>() ) return false;
-
- // localize string from variant
- const string& entireTagFilterString = entireTagFilter.get<string>();
-
- // ensure we have at least "XX:x"
- if ( entireTagFilterString.length() < 4 ) return false;
-
- // get tagName & lookup in alignment
- // if found, set tagType to tag type character
- // if not found, return false
- const string& tagName = entireTagFilterString.substr(0,2);
- char tagType = '\0';
- if ( !al.GetTagType(tagName, tagType) ) return false;
-
- // remove tagName & ":" from beginning tagFilter
- string tagFilterString = entireTagFilterString.substr(3);
-
- // switch on tag type to set tag query value & parse filter token
- int32_t intFilterValue, intQueryValue;
- uint32_t uintFilterValue, uintQueryValue;
- float realFilterValue, realQueryValue;
- string stringFilterValue, stringQueryValue;
-
- PropertyFilterValue tagFilter;
- PropertyFilterValue::ValueCompareType compareType;
- bool keepAlignment = false;
- switch (tagType) {
-
- // signed int tag type
- case 'c' :
- case 's' :
+ // ensure filter contains string data
+ Variant entireTagFilter = valueFilter.Value;
+ if ( !entireTagFilter.is_type<string>() ) return false;
+
+ // localize string from variant
+ const string& entireTagFilterString = entireTagFilter.get<string>();
+
+ // ensure we have at least "XX:x"
+ if ( entireTagFilterString.length() < 4 ) return false;
+
+ // get tagName & lookup in alignment
+ // if found, set tagType to tag type character
+ // if not found, return false
+ const string& tagName = entireTagFilterString.substr(0,2);
+ char tagType = '\0';
+ if ( !al.GetTagType(tagName, tagType) ) return false;
+
+ // remove tagName & ":" from beginning tagFilter
+ string tagFilterString = entireTagFilterString.substr(3);
+
+ // switch on tag type to set tag query value & parse filter token
+ int32_t intFilterValue, intQueryValue;
+ uint32_t uintFilterValue, uintQueryValue;
+ float realFilterValue, realQueryValue;
+ string stringFilterValue, stringQueryValue;
+
+ PropertyFilterValue tagFilter;
+ PropertyFilterValue::ValueCompareType compareType;
+ bool keepAlignment = false;
+ switch (tagType) {
+
+ // signed int tag type
+ case 'c' :
+ case 's' :
case 'i' :
- if ( al.GetTag(tagName, intQueryValue) ) {
- if ( FilterEngine<BamAlignmentChecker>::parseToken(tagFilterString, intFilterValue, compareType) ) {
- tagFilter.Value = intFilterValue;
- tagFilter.Type = compareType;
- keepAlignment = tagFilter.check(intQueryValue);
- }
- }
- break;
-
- // unsigned int tag type
+ if ( al.GetTag(tagName, intQueryValue) ) {
+ if ( FilterEngine<BamAlignmentChecker>::parseToken(tagFilterString, intFilterValue, compareType) ) {
+ tagFilter.Value = intFilterValue;
+ tagFilter.Type = compareType;
+ keepAlignment = tagFilter.check(intQueryValue);
+ }
+ }
+ break;
+
+ // unsigned int tag type
case 'C' :
case 'S' :
- case 'I' :
- if ( al.GetTag(tagName, uintQueryValue) ) {
- if ( FilterEngine<BamAlignmentChecker>::parseToken(tagFilterString, uintFilterValue, compareType) ) {
- tagFilter.Value = uintFilterValue;
- tagFilter.Type = compareType;
- keepAlignment = tagFilter.check(uintQueryValue);
- }
- }
- break;
-
- // 'real' tag type
+ case 'I' :
+ if ( al.GetTag(tagName, uintQueryValue) ) {
+ if ( FilterEngine<BamAlignmentChecker>::parseToken(tagFilterString, uintFilterValue, compareType) ) {
+ tagFilter.Value = uintFilterValue;
+ tagFilter.Type = compareType;
+ keepAlignment = tagFilter.check(uintQueryValue);
+ }
+ }
+ break;
+
+ // 'real' tag type
case 'f' :
- if ( al.GetTag(tagName, realQueryValue) ) {
- if ( FilterEngine<BamAlignmentChecker>::parseToken(tagFilterString, realFilterValue, compareType) ) {
- tagFilter.Value = realFilterValue;
- tagFilter.Type = compareType;
- keepAlignment = tagFilter.check(realQueryValue);
- }
- }
+ if ( al.GetTag(tagName, realQueryValue) ) {
+ if ( FilterEngine<BamAlignmentChecker>::parseToken(tagFilterString, realFilterValue, compareType) ) {
+ tagFilter.Value = realFilterValue;
+ tagFilter.Type = compareType;
+ keepAlignment = tagFilter.check(realQueryValue);
+ }
+ }
break;
-
- // string tag type
+
+ // string tag type
case 'A':
case 'Z':
- case 'H':
+ case 'H':
if ( al.GetTag(tagName, stringQueryValue) ) {
- if ( FilterEngine<BamAlignmentChecker>::parseToken(tagFilterString, stringFilterValue, compareType) ) {
- tagFilter.Value = stringFilterValue;
- tagFilter.Type = compareType;
- keepAlignment = tagFilter.check(stringQueryValue);
- }
- }
- break;
-
- // unknown tag type
- default :
- keepAlignment = false;
- }
-
- return keepAlignment;
+ if ( FilterEngine<BamAlignmentChecker>::parseToken(tagFilterString, stringFilterValue, compareType) ) {
+ tagFilter.Value = stringFilterValue;
+ tagFilter.Type = compareType;
+ keepAlignment = tagFilter.check(stringQueryValue);
+ }
+ }
+ break;
+
+ // unknown tag type
+ default :
+ keepAlignment = false;
+ }
+
+ return keepAlignment;
}
};
// attempt to re-open reader with index files
reader.Close();
- bool openedOK = reader.Open(m_settings->InputFiles, true, false );
+ bool openedOK = reader.Open(m_settings->InputFiles, true, false );
// if error
if ( !openedOK ) {
cerr << "ERROR: Could not open input BAM file(s)... Aborting." << endl;
- return false;
+ return false;
}
// if index data available, we can use SetRegion
if ( !reader.SetRegion(region.LeftRefID, region.LeftPosition, region.RightRefID, region.RightPosition) ) {
cerr << "ERROR: Region requested, but could not set BamReader region to REGION: " << m_settings->Region << " Aborting." << endl;
reader.Close();
- return false;
+ return false;
}
// everything checks out, just iterate through specified region, filtering alignments
- while ( reader.GetNextAlignment(al) )
+ while ( reader.GetNextAlignment(al) )
if ( CheckAlignment(al) )
writer.SaveAlignment(al);
- }
+ }
// no index data available, we have to iterate through until we
// find overlapping alignments
else {
- while ( reader.GetNextAlignment(al) ) {
+ while ( reader.GetNextAlignment(al) ) {
if ( (al.RefID >= region.LeftRefID) && ((al.Position + al.Length) >= region.LeftPosition) &&
(al.RefID <= region.RightRefID) && ( al.Position <= region.RightPosition) )
{
cerr << "ERROR: Could not parse REGION - " << m_settings->Region << endl;
cerr << "Be sure REGION is in valid format (see README) and that coordinates are valid for selected references" << endl;
reader.Close();
- return false;
+ return false;
}
}
projects / bamtools.git / blobdiff