return false;
}
+ // initialize return status
+ bool success = true;
+
// see if root object contains multiple filters
const Json::Value filters = root["filters"];
if ( !filters.isNull() ) {
- bool success = true;
-
// iterate over any filters found
int filterIndex = 0;
Json::Value::const_iterator filtersIter = filters.begin();
Json::Value filter = (*filtersIter);
// convert filter index to string
- stringstream convert;
- convert << filterIndex;
- const string filterName = convert.str();
+ string filterName;
+
+ // if id tag supplied
+ const Json::Value id = filter["id"];
+ if ( !id.isNull() ) {
+ filterName = id.asString();
+ }
+
+ // use array index
+ else {
+ stringstream convert;
+ convert << filterIndex;
+ filterName = convert.str();
+ }
// create & parse filter
success &= ParseFilterObject(filterName, filter);
-
}
+
+ // see if user defined "rule" for these filters
+ const Json::Value rule = root["rule"];
+ if ( !rule.isNull() ) {
+ cout << "found rule: " << rule.asString() << endl;
+ } else {
+ cout << "no rule found!" << endl;
+ }
+
return success;
}
// otherwise, root is the only filter (just contains properties)
// create & parse filter named "ROOT"
- else return ParseFilterObject("ROOT", root);
+ else success = ParseFilterObject("ROOT", root);
+
+ // return success/failure
+ return success;
}
bool writeUncompressed = ( m_settings->OutputFilename == Options::StandardOut() && !m_settings->IsForceCompression );
writer.Open(m_settings->OutputFilename, headerText, m_references, writeUncompressed);
- // set up error handling
- ostringstream errorStream("");
- bool foundError(false);
+ BamAlignment al;
- // if no REGION specified, run filter on entire file contents
+ // if no region specified, filter entire file
if ( !m_settings->HasRegion ) {
- BamAlignment al;
while ( reader.GetNextAlignment(al) ) {
- // perform main filter check
if ( CheckAlignment(al) )
writer.SaveAlignment(al);
}
}
- // REGION specified
+ // otherwise attempt to use region as constraint
else {
-
- // attempt to parse string into BamRegion struct
+
+ // if region string parses OK
BamRegion region;
if ( Utilities::ParseRegionString(m_settings->Region, reader, region) ) {
- // check if there are index files *.bai/*.bti corresponding to the input files
- bool hasDefaultIndex = false;
- bool hasBamtoolsIndex = false;
- bool hasNoIndex = false;
- int defaultIndexCount = 0;
- int bamtoolsIndexCount = 0;
- for (vector<string>::const_iterator f = m_settings->InputFiles.begin(); f != m_settings->InputFiles.end(); ++f) {
-
- if ( Utilities::FileExists(*f + ".bai") ) {
- hasDefaultIndex = true;
- ++defaultIndexCount;
- }
-
- if ( Utilities::FileExists(*f + ".bti") ) {
- hasBamtoolsIndex = true;
- ++bamtoolsIndexCount;
- }
-
- if ( !hasDefaultIndex && !hasBamtoolsIndex ) {
- hasNoIndex = true;
- cerr << "*WARNING - could not find index file for " << *f
- << ", parsing whole file(s) to get alignment counts for target region"
- << " (could be slow)" << endl;
- break;
- }
- }
-
- // determine if index file types are heterogeneous
- bool hasDifferentIndexTypes = false;
- if ( defaultIndexCount > 0 && bamtoolsIndexCount > 0 ) {
- hasDifferentIndexTypes = true;
- cerr << "*WARNING - different index file formats found"
- << ", parsing whole file(s) to get alignment counts for target region"
- << " (could be slow)" << endl;
- }
+ // attempt to re-open reader with index files
+ reader.Close();
+ bool openedOK = reader.Open(m_settings->InputFiles, true, true );
- // if any input file has no index, or if input files use different index formats
- // can't use BamMultiReader to jump directly (**for now**)
- if ( hasNoIndex || hasDifferentIndexTypes ) {
-
- // read through sequentially, but onlt perform filter on reads overlapping REGION
- BamAlignment al;
- while( reader.GetNextAlignment(al) ) {
- if ( (al.RefID >= region.LeftRefID) && ( (al.Position + al.Length) >= region.LeftPosition ) &&
- (al.RefID <= region.RightRefID) && ( al.Position <= region.RightPosition) )
- {
- // perform main filter check
- if ( CheckAlignment(al) )
- writer.SaveAlignment(al);
- }
- }
+ // if error
+ if ( !openedOK ) {
+ cerr << "ERROR: Could not open input BAM file(s)... Aborting." << endl;
+ return 1;
}
- // has index file for each input file (and same format)
- else {
-
- // this is kind of a hack...?
- BamMultiReader reader;
- reader.Open(m_settings->InputFiles, true, true, hasDefaultIndex );
+ // if index data available, we can use SetRegion
+ if ( reader.IsIndexLoaded() ) {
+ // attempt to use SetRegion(), if failed report error
if ( !reader.SetRegion(region.LeftRefID, region.LeftPosition, region.RightRefID, region.RightPosition) ) {
- foundError = true;
- errorStream << "Could not set BamReader region to REGION: " << m_settings->Region << endl;
- } else {
-
- // filter only alignments from specified region
- BamAlignment al;
- while ( reader.GetNextAlignment(al) ) {
- // perform main filter check
+ cerr << "ERROR: Region requested, but could not set BamReader region to REGION: " << m_settings->Region << " Aborting." << endl;
+ reader.Close();
+ return 1;
+ }
+
+ // everything checks out, just iterate through specified region, filtering alignments
+ while ( reader.GetNextAlignmentCore(al) )
+ if ( CheckAlignment(al) )
+ writer.SaveAlignment(al);
+ }
+
+ // no index data available, we have to iterate through until we
+ // find overlapping alignments
+ else {
+ while( reader.GetNextAlignmentCore(al) ) {
+ if ( (al.RefID >= region.LeftRefID) && ( (al.Position + al.Length) >= region.LeftPosition ) &&
+ (al.RefID <= region.RightRefID) && ( al.Position <= region.RightPosition) )
+ {
if ( CheckAlignment(al) )
writer.SaveAlignment(al);
}
}
}
-
- } else {
- foundError = true;
- errorStream << "Could not parse REGION: " << m_settings->Region << endl;
- errorStream << "Be sure REGION is in valid format (see README) and that coordinates are valid for selected references" << endl;
+ }
+
+ // error parsing REGION string
+ else {
+ 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 1;
}
}
projects / bamtools.git / blobdiff