1 // ***************************************************************************
2 // bamtools_sort.cpp (c) 2010 Derek Barnett, Erik Garrison
3 // Marth Lab, Department of Biology, Boston College
4 // All rights reserved.
5 // ---------------------------------------------------------------------------
6 // Last modified: 21 June 2010 (DB)
7 // ---------------------------------------------------------------------------
8 // Sorts an input BAM file (default by position) and stores in a new BAM file.
9 // ***************************************************************************
18 #include "bamtools_sort.h"
19 #include "bamtools_options.h"
20 #include "BamReader.h"
21 #include "BamMultiReader.h"
22 #include "BamWriter.h"
25 using namespace BamTools;
31 // ** These defaults should be tweaked & 'optimized' per testing ** //
32 // I say 'optimized' because each system will naturally perform
33 // differently. We will attempt to determine a sensible
34 // compromise that should perform well on average.
35 const unsigned int SORT_DEFAULT_MAX_BUFFER_COUNT = 10000; // max numberOfAlignments for buffer
36 const unsigned int SORT_DEFAULT_MAX_BUFFER_MEMORY = 1024; // Mb
38 // -----------------------------------
39 // comparison objects (for sorting)
41 struct SortLessThanPosition {
42 bool operator() (const BamAlignment& lhs, const BamAlignment& rhs) {
43 if ( lhs.RefID != rhs.RefID )
44 return lhs.RefID < rhs.RefID;
46 return lhs.Position < rhs.Position;
50 struct SortLessThanName {
51 bool operator() (const BamAlignment& lhs, const BamAlignment& rhs) {
52 return lhs.Name < rhs.Name;
56 } // namespace BamTools
58 // ---------------------------------------------
59 // SortToolPrivate declaration
60 class SortTool::SortToolPrivate {
64 SortToolPrivate(SortTool::SortSettings* settings);
65 ~SortToolPrivate(void);
73 bool GenerateSortedRuns(void);
74 bool HandleBufferContents(vector<BamAlignment>& buffer);
75 bool MergeSortedRuns(void);
76 bool WriteTempFile(const vector<BamAlignment>& buffer, const string& tempFilename);
77 void SortBuffer(vector<BamAlignment>& buffer);
81 SortTool::SortSettings* m_settings;
82 string m_tempFilenameStub;
85 RefVector m_references;
86 vector<string> m_tempFilenames;
89 // ---------------------------------------------
90 // SortSettings implementation
92 struct SortTool::SortSettings {
95 bool HasInputBamFilename;
96 bool HasMaxBufferCount;
97 bool HasMaxBufferMemory;
98 bool HasOutputBamFilename;
102 string InputBamFilename;
103 string OutputBamFilename;
106 unsigned int MaxBufferCount;
107 unsigned int MaxBufferMemory;
111 : HasInputBamFilename(false)
112 , HasMaxBufferCount(false)
113 , HasMaxBufferMemory(false)
114 , HasOutputBamFilename(false)
115 , IsSortingByName(false)
116 , InputBamFilename(Options::StandardIn())
117 , OutputBamFilename(Options::StandardOut())
118 , MaxBufferCount(SORT_DEFAULT_MAX_BUFFER_COUNT)
119 , MaxBufferMemory(SORT_DEFAULT_MAX_BUFFER_MEMORY)
123 // ---------------------------------------------
124 // SortTool implementation
126 SortTool::SortTool(void)
128 , m_settings(new SortSettings)
131 // set program details
132 Options::SetProgramInfo("bamtools sort", "sorts a BAM file", "[-in <filename>] [-out <filename>]");
135 OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
136 Options::AddValueOption("-in", "BAM filename", "the input BAM file", "", m_settings->HasInputBamFilename, m_settings->InputBamFilename, IO_Opts, Options::StandardIn());
137 Options::AddValueOption("-out", "BAM filename", "the output BAM file", "", m_settings->HasOutputBamFilename, m_settings->OutputBamFilename, IO_Opts, Options::StandardOut());
139 OptionGroup* SortOpts = Options::CreateOptionGroup("Sorting Methods");
140 Options::AddOption("-byname", "sort by alignment name", m_settings->IsSortingByName, SortOpts);
142 OptionGroup* MemOpts = Options::CreateOptionGroup("Memory Settings");
143 Options::AddValueOption("-n", "count", "max number of alignments per tempfile", "", m_settings->HasMaxBufferCount, m_settings->MaxBufferCount, MemOpts, SORT_DEFAULT_MAX_BUFFER_COUNT);
144 Options::AddValueOption("-mem", "Mb", "max memory to use", "", m_settings->HasMaxBufferMemory, m_settings->MaxBufferMemory, MemOpts, SORT_DEFAULT_MAX_BUFFER_MEMORY);
147 SortTool::~SortTool(void) {
156 int SortTool::Help(void) {
157 Options::DisplayHelp();
161 int SortTool::Run(int argc, char* argv[]) {
163 // parse command line arguments
164 Options::Parse(argc, argv, 1);
166 // run internal SortTool implementation, return success/fail
167 m_impl = new SortToolPrivate(m_settings);
169 if ( m_impl->Run() ) return 0;
173 // ---------------------------------------------
174 // SortToolPrivate implementation
177 SortTool::SortToolPrivate::SortToolPrivate(SortTool::SortSettings* settings)
178 : m_settings(settings)
181 // set filename stub depending on inputfile path
182 // that way multiple sort runs don't trip on each other's temp files
184 size_t extensionFound = m_settings->InputBamFilename.find(".bam");
185 if (extensionFound != string::npos )
186 m_tempFilenameStub = m_settings->InputBamFilename.substr(0,extensionFound);
187 m_tempFilenameStub.append(".sort.temp.");
192 SortTool::SortToolPrivate::~SortToolPrivate(void) { }
194 // generates mutiple sorted temp BAM files from single unsorted BAM file
195 bool SortTool::SortToolPrivate::GenerateSortedRuns(void) {
197 // open input BAM file
198 BamReader inputReader;
199 inputReader.Open(m_settings->InputBamFilename);
201 // get basic data that will be shared by all temp/output files
202 m_headerText = inputReader.GetHeaderText();
203 m_references = inputReader.GetReferenceData();
205 // set up alignments buffer
206 vector<BamAlignment> buffer;
207 buffer.reserve(m_settings->MaxBufferCount);
209 // while data available
211 while ( inputReader.GetNextAlignmentCore(al) ) {
213 // store alignments in buffer
214 buffer.push_back(al);
216 // if buffer is full, handle contents (sort & write to temp file)
217 if ( buffer.size() == m_settings->MaxBufferCount )
218 HandleBufferContents(buffer);
221 // handle any remaining buffer contents
222 if ( buffer.size() > 0 )
223 HandleBufferContents(buffer);
225 // close reader & return success
230 bool SortTool::SortToolPrivate::HandleBufferContents(vector<BamAlignment>& buffer ) {
235 // write sorted contents to temp file, store success/fail
236 stringstream tempStr;
237 tempStr << m_tempFilenameStub << m_numberOfRuns;
238 bool success = WriteTempFile( buffer, tempStr.str() );
240 // save temp filename for merging later
241 m_tempFilenames.push_back(tempStr.str());
243 // clear buffer contents & update run counter
247 // return success/fail of writing to temp file
251 // merges sorted temp BAM files into single sorted output BAM file
252 bool SortTool::SortToolPrivate::MergeSortedRuns(void) {
254 // open up multi reader for all of our temp files
255 // this might get broken up if we do a multi-pass system later ??
256 BamMultiReader multiReader;
257 multiReader.Open(m_tempFilenames, false, true);
259 // open writer for our completely sorted output BAM file
260 BamWriter mergedWriter;
261 mergedWriter.Open(m_settings->OutputBamFilename, m_headerText, m_references);
263 // while data available in temp files
265 while ( multiReader.GetNextAlignment(al) ) {
266 mergedWriter.SaveAlignment(al);
271 mergedWriter.Close();
273 // delete all temp files
274 vector<string>::const_iterator tempIter = m_tempFilenames.begin();
275 vector<string>::const_iterator tempEnd = m_tempFilenames.end();
276 for ( ; tempIter != tempEnd; ++tempIter ) {
277 const string& tempFilename = (*tempIter);
278 remove(tempFilename.c_str());
284 bool SortTool::SortToolPrivate::Run(void) {
286 // this does a single pass, chunking up the input file into smaller sorted temp files,
287 // then write out using BamMultiReader to handle merging
289 if ( GenerateSortedRuns() )
290 return MergeSortedRuns();
295 void SortTool::SortToolPrivate::SortBuffer(vector<BamAlignment>& buffer) {
297 // ** add further custom sort options later ?? **
299 // sort buffer by desired method
300 if ( m_settings->IsSortingByName )
301 sort ( buffer.begin(), buffer.end(), SortLessThanName() );
303 sort ( buffer.begin(), buffer.end(), SortLessThanPosition() );
307 bool SortTool::SortToolPrivate::WriteTempFile(const vector<BamAlignment>& buffer, const string& tempFilename) {
309 // open temp file for writing
310 BamWriter tempWriter;
311 tempWriter.Open(tempFilename, m_headerText, m_references);
314 vector<BamAlignment>::const_iterator buffIter = buffer.begin();
315 vector<BamAlignment>::const_iterator buffEnd = buffer.end();
316 for ( ; buffIter != buffEnd; ++buffIter ) {
317 const BamAlignment& al = (*buffIter);
318 tempWriter.SaveAlignment(al);
321 // close temp file & return success