// Marth Lab, Department of Biology, Boston College
// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 21 June 2010 (DB)
+// Last modified: 21 March 2011 (DB)
// ---------------------------------------------------------------------------
// Sorts an input BAM file (default by position) and stores in a new BAM file.
// ***************************************************************************
+#include "bamtools_sort.h"
+
+#include <api/SamConstants.h>
+#include <api/BamMultiReader.h>
+#include <api/BamWriter.h>
+#include <utils/bamtools_options.h>
+using namespace BamTools;
+
#include <cstdio>
#include <algorithm>
#include <iostream>
#include <sstream>
#include <string>
#include <vector>
-
-#include "bamtools_sort.h"
-#include "bamtools_options.h"
-#include "BamReader.h"
-#include "BamMultiReader.h"
-#include "BamWriter.h"
-
using namespace std;
-using namespace BamTools;
namespace BamTools {
// defaults
//
// ** These defaults should be tweaked & 'optimized' per testing ** //
+ //
// I say 'optimized' because each system will naturally perform
// differently. We will attempt to determine a sensible
// compromise that should perform well on average.
- const unsigned int SORT_DEFAULT_MAX_BUFFER_COUNT = 10000; // max numberOfAlignments for buffer
- const unsigned int SORT_DEFAULT_MAX_BUFFER_MEMORY = 1024; // Mb
+ const unsigned int SORT_DEFAULT_MAX_BUFFER_COUNT = 500000; // max numberOfAlignments for buffer
+ const unsigned int SORT_DEFAULT_MAX_BUFFER_MEMORY = 1024; // Mb
// -----------------------------------
// comparison objects (for sorting)
, m_impl(0)
{
// set program details
- Options::SetProgramInfo("bamtools sort", "sorts a BAM file", "[-in <filename>] [-out <filename>]");
+ Options::SetProgramInfo("bamtools sort", "sorts a BAM file", "[-in <filename>] [-out <filename>] [sortOptions]");
// set up options
OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
// open input BAM file
BamReader inputReader;
- if (!inputReader.Open(m_settings->InputBamFilename)) {
- cerr << "Could not open " << m_settings->InputBamFilename << " for reading." << endl;
+ if ( !inputReader.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
- m_headerText = inputReader.GetHeaderText();
+ SamHeader header = inputReader.GetHeader();
+ header.SortOrder = ( m_settings->IsSortingByName
+ ? Constants::SAM_HD_SORTORDER_QUERYNAME
+ : Constants::SAM_HD_SORTORDER_COORDINATE );
+ m_headerText = header.ToString();
m_references = inputReader.GetReferenceData();
// set up alignments buffer
+ BamAlignment al;
vector<BamAlignment> buffer;
buffer.reserve(m_settings->MaxBufferCount);
- // while data available
- BamAlignment al;
- 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);
+ // 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);
+ }
+
}
-
+
+ // 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);
+ }
+ }
+
// handle any remaining buffer contents
if ( buffer.size() > 0 )
HandleBufferContents(buffer);
++m_numberOfRuns;
// return success/fail of writing to temp file
+ // TODO: a failure returned here is not actually caught and handled anywhere
return success;
}
// open up multi reader for all of our temp files
// this might get broken up if we do a multi-pass system later ??
BamMultiReader multiReader;
- multiReader.Open(m_tempFilenames, false, true);
+ if ( !multiReader.Open(m_tempFilenames) ) {
+ cerr << "bamtools sort ERROR: could not open BamMultiReader for merging temp files... Aborting." << endl;
+ return false;
+ }
+
+ // set sort order for merge
+ if ( m_settings->IsSortingByName )
+ multiReader.SetSortOrder(BamMultiReader::SortedByReadName);
+ else
+ multiReader.SetSortOrder(BamMultiReader::SortedByPosition);
// open writer for our completely sorted output BAM file
BamWriter mergedWriter;
- mergedWriter.Open(m_settings->OutputBamFilename, m_headerText, m_references);
+ if ( !mergedWriter.Open(m_settings->OutputBamFilename, m_headerText, m_references) ) {
+ cerr << "bamtools sort ERROR: could not open " << m_settings->OutputBamFilename
+ << " for writing... Aborting." << endl;
+ multiReader.Close();
+ return false;
+ }
// while data available in temp files
BamAlignment al;
- while ( multiReader.GetNextAlignmentCore(al) ) {
+ while ( multiReader.GetNextAlignmentCore(al) )
mergedWriter.SaveAlignment(al);
- }
// close readers
multiReader.Close();
// open temp file for writing
BamWriter tempWriter;
- tempWriter.Open(tempFilename, m_headerText, m_references);
+ if ( !tempWriter.Open(tempFilename, m_headerText, m_references) ) {
+ cerr << "bamtools sort ERROR: could not open " << tempFilename
+ << " for writing." << endl;
+ return false;
+ }
// write data
vector<BamAlignment>::const_iterator buffIter = buffer.begin();
projects / bamtools.git / blobdiff