// ***************************************************************************
// bamtools_sort.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 7 April 2011 (DB)
+// Last modified: 28 September 2011 (DB)
// ---------------------------------------------------------------------------
// Sorts an input BAM file
// ***************************************************************************
struct SortLessThanPosition {
bool operator() (const BamAlignment& lhs, const BamAlignment& rhs) {
+
+ // force unmapped alignments to end
+ if ( lhs.RefID == -1 ) return false;
+ if ( rhs.RefID == -1 ) return true;
+
+ // sort first on RefID, then by Position
if ( lhs.RefID != rhs.RefID )
return lhs.RefID < rhs.RefID;
else
// internal methods
private:
- void ClearBuffer(vector<BamAlignment>& buffer);
+ bool CreateSortedTempFile(vector<BamAlignment>& buffer);
bool GenerateSortedRuns(void);
- bool HandleBufferContents(vector<BamAlignment>& buffer);
bool MergeSortedRuns(void);
bool WriteTempFile(const vector<BamAlignment>& buffer, const string& tempFilename);
void SortBuffer(vector<BamAlignment>& buffer);
vector<string> m_tempFilenames;
};
-
// constructor
SortTool::SortToolPrivate::SortToolPrivate(SortTool::SortSettings* settings)
: m_settings(settings)
bool SortTool::SortToolPrivate::GenerateSortedRuns(void) {
// open input BAM file
- BamReader inputReader;
- if ( !inputReader.Open(m_settings->InputBamFilename) ) {
+ BamReader reader;
+ if ( !reader.Open(m_settings->InputBamFilename) ) {
cerr << "bamtools sort ERROR: could not open " << m_settings->InputBamFilename
<< " for reading... Aborting." << endl;
return false;
}
// get basic data that will be shared by all temp/output files
- SamHeader header = inputReader.GetHeader();
+ SamHeader header = reader.GetHeader();
header.SortOrder = ( m_settings->IsSortingByName
? Constants::SAM_HD_SORTORDER_QUERYNAME
: Constants::SAM_HD_SORTORDER_COORDINATE );
m_headerText = header.ToString();
- m_references = inputReader.GetReferenceData();
+ m_references = reader.GetReferenceData();
// set up alignments buffer
BamAlignment al;
vector<BamAlignment> buffer;
- buffer.reserve(m_settings->MaxBufferCount);
+ buffer.reserve( (size_t)(m_settings->MaxBufferCount*1.1) );
+ bool bufferFull = false;
// if sorting by name, we need to generate full char data
// so can't use GetNextAlignmentCore()
if ( m_settings->IsSortingByName ) {
// iterate through file
- while ( inputReader.GetNextAlignment(al)) {
-
- // store alignments in buffer
- buffer.push_back(al);
-
- // if buffer is full, handle contents (sort & write to temp file)
- if ( buffer.size() == m_settings->MaxBufferCount )
- HandleBufferContents(buffer);
+ while ( reader.GetNextAlignment(al)) {
+
+ // check buffer's usage
+ bufferFull = ( buffer.size() >= m_settings->MaxBufferCount );
+
+ // store alignments until buffer is "full"
+ if ( !bufferFull )
+ buffer.push_back(al);
+
+ // if buffer is "full"
+ else {
+
+ // push any unmapped reads into buffer,
+ // don't want to split these into a separate temp file
+ if ( !al.IsMapped() )
+ buffer.push_back(al);
+
+ // "al" is mapped, so create a sorted temp file with current buffer contents
+ // then push "al" into fresh buffer
+ else {
+ CreateSortedTempFile(buffer);
+ buffer.push_back(al);
+ }
+ }
}
-
}
// sorting by position, can take advantage of GNACore() speedup
else {
// iterate through file
- while ( inputReader.GetNextAlignmentCore(al) ) {
-
- // store alignments in buffer
- buffer.push_back(al);
-
- // if buffer is full, handle contents (sort & write to temp file)
- if ( buffer.size() == m_settings->MaxBufferCount )
- HandleBufferContents(buffer);
+ while ( reader.GetNextAlignmentCore(al) ) {
+
+ // check buffer's usage
+ bufferFull = ( buffer.size() >= m_settings->MaxBufferCount );
+
+ // store alignments until buffer is "full"
+ if ( !bufferFull )
+ buffer.push_back(al);
+
+ // if buffer is "full"
+ else {
+
+ // push any unmapped reads into buffer,
+ // don't want to split these into a separate temp file
+ if ( !al.IsMapped() )
+ buffer.push_back(al);
+
+ // "al" is mapped, so create a sorted temp file with current buffer contents
+ // then push "al" into fresh buffer
+ else {
+ CreateSortedTempFile(buffer);
+ buffer.push_back(al);
+ }
+ }
}
}
- // handle any remaining buffer contents
- if ( buffer.size() > 0 )
- HandleBufferContents(buffer);
+ // handle any leftover buffer contents
+ if ( !buffer.empty() )
+ CreateSortedTempFile(buffer);
// close reader & return success
- inputReader.Close();
+ reader.Close();
return true;
}
-bool SortTool::SortToolPrivate::HandleBufferContents(vector<BamAlignment>& buffer ) {
+bool SortTool::SortToolPrivate::CreateSortedTempFile(vector<BamAlignment>& buffer) {
// do sorting
SortBuffer(buffer);
// this might get broken up if we do a multi-pass system later ??
BamMultiReader multiReader;
if ( !multiReader.Open(m_tempFilenames) ) {
- cerr << "bamtools sort ERROR: could not open BamMultiReader for merging temp files... Aborting." << endl;
+ cerr << "bamtools sort ERROR: could not open BamMultiReader for merging temp files... Aborting."
+ << endl;
return false;
}
// sort buffer by desired method
if ( m_settings->IsSortingByName )
- sort ( buffer.begin(), buffer.end(), SortLessThanName() );
+ std::stable_sort ( buffer.begin(), buffer.end(), SortLessThanName() );
else
- sort ( buffer.begin(), buffer.end(), SortLessThanPosition() );
+ std::stable_sort ( buffer.begin(), buffer.end(), SortLessThanPosition() );
}
-
-bool SortTool::SortToolPrivate::WriteTempFile(const vector<BamAlignment>& buffer, const string& tempFilename) {
-
+bool SortTool::SortToolPrivate::WriteTempFile(const vector<BamAlignment>& buffer,
+ const string& tempFilename)
+{
// open temp file for writing
BamWriter tempWriter;
if ( !tempWriter.Open(tempFilename, m_headerText, m_references) ) {
// 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("-out", "BAM filename", "the output BAM file", "", m_settings->HasOutputBamFilename, m_settings->OutputBamFilename, IO_Opts, Options::StandardOut());
+ Options::AddValueOption("-in", "BAM filename", "the input BAM file", "",
+ m_settings->HasInputBamFilename, m_settings->InputBamFilename,
+ IO_Opts, Options::StandardIn());
+ Options::AddValueOption("-out", "BAM filename", "the output BAM file", "",
+ m_settings->HasOutputBamFilename, m_settings->OutputBamFilename,
+ IO_Opts, Options::StandardOut());
OptionGroup* SortOpts = Options::CreateOptionGroup("Sorting Methods");
Options::AddOption("-byname", "sort by alignment name", m_settings->IsSortingByName, SortOpts);
OptionGroup* MemOpts = Options::CreateOptionGroup("Memory Settings");
- Options::AddValueOption("-n", "count", "max number of alignments per tempfile", "", m_settings->HasMaxBufferCount, m_settings->MaxBufferCount, MemOpts, SORT_DEFAULT_MAX_BUFFER_COUNT);
- Options::AddValueOption("-mem", "Mb", "max memory to use", "", m_settings->HasMaxBufferMemory, m_settings->MaxBufferMemory, MemOpts, SORT_DEFAULT_MAX_BUFFER_MEMORY);
+ Options::AddValueOption("-n", "count", "max number of alignments per tempfile", "",
+ m_settings->HasMaxBufferCount, m_settings->MaxBufferCount,
+ MemOpts, SORT_DEFAULT_MAX_BUFFER_COUNT);
+ Options::AddValueOption("-mem", "Mb", "max memory to use", "",
+ m_settings->HasMaxBufferMemory, m_settings->MaxBufferMemory,
+ MemOpts, SORT_DEFAULT_MAX_BUFFER_MEMORY);
}
SortTool::~SortTool(void) {
projects / bamtools.git / blobdiff