, m_settings(new CountSettings)
{
// set program details
- Options::SetProgramInfo("bamtools count", "prints alignment counts for a BAM file", "-in <filename> [-region REGION -index <filename>]");
+ Options::SetProgramInfo("bamtools count", "prints alignment counts for a BAM file", "-in <filename> [-region <REGION> [-index <filename>]]");
// set up options
OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
- Options::AddValueOption("-in", "BAM filename", "the input BAM file", "", m_settings->HasInputBamFilename, m_settings->InputBamFilename, IO_Opts, Options::StandardIn());
- Options::AddValueOption("-index", "BAM index filename", "the BAM index file", "", m_settings->HasBamIndexFilename, m_settings->BamIndexFilename, IO_Opts);
+ Options::AddValueOption("-in", "BAM filename", "the input BAM file", "", m_settings->HasInputBamFilename, m_settings->InputBamFilename, IO_Opts, Options::StandardIn());
+ Options::AddValueOption("-index", "BAM index filename", "the BAM index file", "", m_settings->HasBamIndexFilename, m_settings->BamIndexFilename, IO_Opts);
OptionGroup* FilterOpts = Options::CreateOptionGroup("Filters");
- Options::AddValueOption("-region", "REGION", "genomic region. Index file is recommended for optimal performance.", "", m_settings->HasRegion, m_settings->Region, FilterOpts);
+ Options::AddValueOption("-region", "REGION", "genomic region. Index file is recommended for better performance. See \'bamtools help index\' for more details on creating one", "", m_settings->HasRegion, m_settings->Region, FilterOpts);
}
CountTool::~CountTool(void) {
BamAlignment al;
while ( reader.GetNextAlignment(al) )
++alignmentCount;
- } else {
+ }
+
+ // more complicated - region specified
+ else {
- // parse region string for desired region
- string startChrom;
- string stopChrom;
- int startPos;
- int stopPos;
- if ( Utilities::ParseRegionString(m_settings->Region, startChrom, startPos, stopChrom, stopPos) ) {
-
- const RefVector references = reader.GetReferenceData();
+ Region region;
+ if ( Utilities::ParseRegionString(m_settings->Region, reader, region) ) {
- // -------------------------------
- // validate start ref & position
-
- int startRefID = reader.GetReferenceID(startChrom);
- cout << "startRefID: " << startRefID << endl;
-
- // startRefID not found
- if ( startRefID == (int)references.size() ) {
- foundError = true;
- errorStream << "Start chrom: " << startChrom << " not found in BAM file." << endl;
- }
-
- // valid startRefID, check startPos
- else {
- const RefData& reference = references.at(startRefID);
-
- // startPos too large
- if ( startPos > reference.RefLength ) {
+ // has index, we can jump directly to
+ if ( m_settings->HasBamIndexFilename ) {
+
+ // this is kind of a hack...?
+ // re-open BamReader, this time with the index file
+ reader.Close();
+ reader.Open(m_settings->InputBamFilename, m_settings->BamIndexFilename);
+
+ // attempt Jump(), catch error
+ if ( !reader.Jump(region.StartChromID, region.StartPosition) ) {
foundError = true;
- errorStream << "Start pos: " << startPos << " is larger than expected." << endl;
+ errorStream << "Could not jump to desired REGION: " << m_settings->Region << endl;
}
}
- // -------------------------------
- // validate stop ref & position
-
- int stopRefID = reader.GetReferenceID(stopChrom);
-
- // skip if error already found
- if ( !foundError ) {
+ else {
- // stopRefID not found
- if ( stopRefID == (int)references.size() ) {
- foundError = true;
- errorStream << "Stop chrom: " << stopChrom << " not found in BAM file." << endl;
- }
-
- // valid stopRefID, check stopPos
- else {
- const RefData& reference = references.at(stopRefID);
-
- // stopPos too large
- if ( stopPos > reference.RefLength ) {
- foundError = true;
- errorStream << "Stop pos: " << stopPos << " is larger than expected." << endl;
- }
-
- // no stopPos specified, set to reference end
- else if ( stopPos == -1 ) {
- stopPos = reference.RefLength;
- }
+ // read through sequentially, until first overlapping read is found
+ BamAlignment al;
+ bool alignmentFound(false);
+ while( reader.GetNextAlignment(al) ) {
+ if ( (al.RefID == region.StartChromID ) && ( (al.Position + al.Length) >= region.StartPosition) ) {
+ alignmentFound = true;
+ break;
+ }
}
+
+ // if overlapping alignment found (not EOF), increment counter
+ if ( alignmentFound) ++ alignmentCount;
}
-
- // -------------------------------
- // if refs & positions valid, retrieve data
+
+ // -----------------------------
+ // count alignments until stop hit
if ( !foundError ) {
-
- // has index, we can jump directly to
- if ( m_settings->HasBamIndexFilename ) {
-
- // this is kind of a hack...?
- // re-open BamReader, this time with the index file
- reader.Close();
- reader.Open(m_settings->InputBamFilename, m_settings->BamIndexFilename);
-
- // attempt Jump(), catch error
- if ( !reader.Jump(startRefID, startPos) ) {
- foundError = true;
- errorStream << "Could not jump to desired REGION: " << m_settings->Region << endl;
- }
- }
-
- else {
-
- // read through sequentially, until first overlapping read is found
- BamAlignment al;
- bool alignmentFound(false);
- while( reader.GetNextAlignment(al) ) {
- if ( (al.RefID == startRefID ) && ( (al.Position + al.Length) >= startPos) ) {
- alignmentFound = true;
- break;
- }
- }
-
- // if overlapping alignment found (not EOF), increment counter
- if ( alignmentFound) ++ alignmentCount;
- }
-
- // -----------------------------
- // count alignments until
-
- if ( !foundError ) {
- // while valid alignment AND
- // ( either current ref is before stopRefID OR
- // current ref stopRefID but we're before stopPos )
- BamAlignment al;
- while ( reader.GetNextAlignment(al) && ((al.RefID < stopRefID ) || (al.RefID == stopRefID && al.Position <= stopPos)) )
- ++alignmentCount;
- }
+ // while valid alignment AND
+ // ( either current ref is before stopRefID OR
+ // current ref stopRefID but we're before stopPos )
+ BamAlignment al;
+ while ( reader.GetNextAlignment(al) && ((al.RefID < region.StopChromID ) || (al.RefID == region.StopChromID && al.Position <= region.StopPosition)) )
+ ++alignmentCount;
}
- }
-
- // could not parse REGION string, set error
- else {
+
+ } else {
foundError = true;
- errorStream << "Could not parse desired REGION: " << m_settings->Region << endl;
- errorStream << "Please see README for details on accepted REGION formats" << endl;
+ 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;
}
}
projects / bamtools.git / blobdiff