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commit b98c0172a28e89f2ecaeddcbddfcc6b927590ca5 Author: Andreas Tille <[email protected]> Date: Sat Feb 10 08:35:11 2018 +0100 Refresh patches --- .../do_not_let_random_failure_tests_fail.patch | 3 + debian/patches/fix_test_script.patch | 2 +- debian/patches/reproducible_build.patch | 2 +- debian/patches/series | 2 +- debian/patches/v2.26.0-19-g6bf23c4.patch | 6700 +------------------- 5 files changed, 33 insertions(+), 6676 deletions(-) diff --git a/debian/patches/do_not_let_random_failure_tests_fail.patch b/debian/patches/do_not_let_random_failure_tests_fail.patch index 2a8afb7..3013aba 100644 --- a/debian/patches/do_not_let_random_failure_tests_fail.patch +++ b/debian/patches/do_not_let_random_failure_tests_fail.patch @@ -2,6 +2,9 @@ Author: Andreas Tille <[email protected]> Last-Update: Sat, 14 Jan 2017 16:10:04 +0100 Bug-Debian: https://bugs.debian.org/747337 Description: Ignore failures in the split feature for the moment +Remark: This patch is deactivated since the upstream test suite changed but + may be we need some reference to what tests needed exclusion and + thus it is left here for the moment --- a/test/test.sh +++ b/test/test.sh diff --git a/debian/patches/fix_test_script.patch b/debian/patches/fix_test_script.patch index 79bd5e9..cc4c60d 100644 --- a/debian/patches/fix_test_script.patch +++ b/debian/patches/fix_test_script.patch @@ -4,7 +4,7 @@ Description: Use environment variable to find bedtools in all cases --- a/test/merge/test-merge.sh +++ b/test/merge/test-merge.sh -@@ -445,7 +445,7 @@ chr1 30 100 .,.,. +@@ -467,7 +467,7 @@ chr1 30 100 .,.,. chr2 10 20 . chr2 30 40 . chr2 42 100 .,." >exp diff --git a/debian/patches/reproducible_build.patch b/debian/patches/reproducible_build.patch index afcac80..8f7fe3b 100644 --- a/debian/patches/reproducible_build.patch +++ b/debian/patches/reproducible_build.patch @@ -5,7 +5,7 @@ Description: Enable reproducible builds --- a/Makefile +++ b/Makefile -@@ -99,7 +99,7 @@ UTIL_SUBDIRS = $(SRC_DIR)/utils/FileReco +@@ -107,7 +107,7 @@ UTIL_SUBDIRS = $(SRC_DIR)/utils/FileReco $(SRC_DIR)/utils/ToolBase \ $(SRC_DIR)/utils/driver diff --git a/debian/patches/series b/debian/patches/series index 2426b50..3a40b3d 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -3,4 +3,4 @@ fix_test_script.patch remove_barski_binding_site.png.patch reproducible_build.patch v2.26.0-19-g6bf23c4.patch -do_not_let_random_failure_tests_fail.patch +# do_not_let_random_failure_tests_fail.patch diff --git a/debian/patches/v2.26.0-19-g6bf23c4.patch b/debian/patches/v2.26.0-19-g6bf23c4.patch index 150225f..e24c108 100644 --- a/debian/patches/v2.26.0-19-g6bf23c4.patch +++ b/debian/patches/v2.26.0-19-g6bf23c4.patch @@ -5,6633 +5,33 @@ Description: Sync with upstream repo at commit 6bf23c In particular, it repairs the groupby command, which was completely broken. Cherry-picking a single commit did not result in a buildable source, and this big patch was the easiest alternative. -diff --git a/Makefile b/Makefile -index 91cbbd5..80c5656 100644 ---- a/Makefile -+++ b/Makefile -@@ -18,7 +18,7 @@ export SRC_DIR = src - export UTIL_DIR = src/utils - export CXX = g++ - ifeq ($(DEBUG),1) --export CXXFLAGS = -Wall -O0 -g -fno-inline -fkeep-inline-functions -D_FILE_OFFSET_BITS=64 -fPIC -DDEBUG -D_DEBUG -+export CXXFLAGS = -Wall -Wextra -DDEBUG -D_DEBUG -g -O0 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES) - else - export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES) - endif -diff --git a/docs/content/history.rst b/docs/content/history.rst -index c59e84e..ac04a02 100644 ---- a/docs/content/history.rst -+++ b/docs/content/history.rst -@@ -4,23 +4,24 @@ Release History - - Version 2.26.0 (7-July-2016) - ============================ --1. Fixed a major memory leak when using ``-sorted``. Thanks to Emily Tsang and Steohen Montgomery. -+1. Fixed a major memory leak when using ``-sorted``. Thanks to Emily Tsang and Stephen Montgomery. - 2. Fixed a bug for BED files containing a single record with no newline. Thanks to @jmarshall. --3. The ``getfasta`` tool includes name, chromosome and position in fasta headers when the ``-name`` option is used. Thanks to @rishavray. --4. Fixed a bug that now forces the ``coverage`` tool to process every record in the ``-a`` file. --5. Fixed a bug preventing proper processing of BED files with consecutive tabs. --6. VCF files containing structural variants now infer SV length from either the SVLEN or END INFO fields. Thanks to Zev Kronenberg. --7. Resolve off by one bugs when intersecting GFF or VCF files with BED files. --8. The ``shuffle`` tool now uses roulette wheel sampling to shuffle to ``-incl`` regions based upon the size of the interval. Thanks to Zev Kronenberg and Michael Imbeault. --9. Fixed a bug in ``coverage`` that prevented correct calculation of depth when using the ``-split`` option. --10. The ``shuffle`` tool warns when an interval exceeds the maximum chromosome length. --11. The ``complement`` tool better checks intervals against the chromosome lengths. --12. Fixes for ``stddev``, ``min``, and ``max`` operations. Thanks to @jmarshall. --13. Enabled ``stdev``, ``sstdev``, ``freqasc``, and ``freqdesc`` options for ``groupby``. --14. Allow ``-s`` and ``-w`` to be used in any order for ``makewindows``. --15. Added new ``-bedOut`` option to ``getfasta``. --16. The ``-r`` option forces the ``-F`` value for ``intersect``. --17. Add ``-pc`` option to the ``genomecov`` tool, allowing coverage to be calculated based upon paired-end fragments. -+3. Fixed a bug in the contigency table values for thr ``fisher`` tool. -+4. The ``getfasta`` tool includes name, chromosome and position in fasta headers when the ``-name`` option is used. Thanks to @rishavray. -+5. Fixed a bug that now forces the ``coverage`` tool to process every record in the ``-a`` file. -+6. Fixed a bug preventing proper processing of BED files with consecutive tabs. -+7. VCF files containing structural variants now infer SV length from either the SVLEN or END INFO fields. Thanks to Zev Kronenberg. -+8. Resolve off by one bugs when intersecting GFF or VCF files with BED files. -+9. The ``shuffle`` tool now uses roulette wheel sampling to shuffle to ``-incl`` regions based upon the size of the interval. Thanks to Zev Kronenberg and Michael Imbeault. -+10. Fixed a bug in ``coverage`` that prevented correct calculation of depth when using the ``-split`` option. -+11. The ``shuffle`` tool warns when an interval exceeds the maximum chromosome length. -+12. The ``complement`` tool better checks intervals against the chromosome lengths. -+13. Fixes for ``stddev``, ``min``, and ``max`` operations. Thanks to @jmarshall. -+14. Enabled ``stdev``, ``sstdev``, ``freqasc``, and ``freqdesc`` options for ``groupby``. -+15. Allow ``-s`` and ``-w`` to be used in any order for ``makewindows``. -+16. Added new ``-bedOut`` option to ``getfasta``. -+17. The ``-r`` option forces the ``-F`` value for ``intersect``. -+18. Add ``-pc`` option to the ``genomecov`` tool, allowing coverage to be calculated based upon paired-end fragments. - - - Version 2.25.0 (3-Sept-2015) -diff --git a/docs/index.rst b/docs/index.rst -index 2d67581..67cdd91 100755 ---- a/docs/index.rst -+++ b/docs/index.rst -@@ -11,6 +11,7 @@ genomic file formats such as BAM, BED, GFF/GTF, VCF. While each individual tool - *intersect* two interval files), quite sophisticated analyses can be conducted - by combining multiple bedtools operations on the UNIX command line. - -+**bedtools** is developed in the `Quinlan laboratory <http://quinlanlab.org>`_ at the `University of Utah <http://www.utah.edu/>`_ and benefits from fantastic contributions made by scientists worldwide. - - ========================== - Tutorial -diff --git a/docs/templates/sidebar-intro.html b/docs/templates/sidebar-intro.html -index 262da46..dc430e7 100644 ---- a/docs/templates/sidebar-intro.html -+++ b/docs/templates/sidebar-intro.html -@@ -8,7 +8,7 @@ - <li><a target="_blank" href="https://bedtools.googlecode.com";>Old Releases @ Google Code</a></li> - <li><a target="_blank" href="http://groups.google.com/group/bedtools-discuss";>Mailing list @ Google Groups</a></li> - <li><a target="_blank" href="http://www.biostars.org/show/tag/bedtools/";>Queries @ Biostar</a></li> -- <li><a target="_blank" href="http://quinlanlab.org";>Quinlan lab @ UVa</a></li> -+ <li><a target="_blank" href="http://quinlanlab.org";>Quinlan lab @ UU</a></li> - - </ul> - -diff --git a/src/bedtools.cpp b/src/bedtools.cpp -index 088ea70..b03b072 100644 ---- a/src/bedtools.cpp -+++ b/src/bedtools.cpp -@@ -34,8 +34,8 @@ using namespace std; - // define our parameter checking macro - #define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen) - --bool sub_main(const QuickString &subCmd); --void showHelp(const QuickString &subCmd); -+bool sub_main(const string &subCmd); -+void showHelp(const string &subCmd); - - int annotate_main(int argc, char* argv[]);// - int bamtobed_main(int argc, char* argv[]);// -@@ -92,7 +92,7 @@ int main(int argc, char *argv[]) - // make sure the user at least entered a sub_command - if (argc < 2) return bedtools_help(); - -- QuickString subCmd(argv[1]); -+ string subCmd(argv[1]); - BedtoolsDriver btDriver; - if (btDriver.supports(subCmd)) { - -@@ -190,8 +190,13 @@ int main(int argc, char *argv[]) - - int bedtools_help(void) - { -- cout << PROGRAM_NAME << ": flexible tools for genome arithmetic and DNA sequence analysis.\n"; -- cout << "usage: bedtools <subcommand> [options]" << endl << endl; -+ cout << PROGRAM_NAME << " is a powerful toolset for genome arithmetic." << endl << endl; -+ cout << "Version: " << VERSION << endl; -+ cout << "About: developed in the quinlanlab.org and by many contributors worldwide." << endl; -+ cout << "Docs: http://bedtools.readthedocs.io/"; << endl; -+ cout << "Code: https://github.com/arq5x/bedtools2"; << endl; -+ cout << "Mail: https://groups.google.com/forum/#!forum/bedtools-discuss"; << endl << endl; -+ cout << "Usage: bedtools <subcommand> [options]" << endl << endl; - - cout << "The bedtools sub-commands include:" << endl; - -@@ -287,7 +292,7 @@ int bedtools_faq(void) - return 0; - } - --void showHelp(const QuickString &subCmd) { -+void showHelp(const string &subCmd) { - if (subCmd == "intersect") { - intersect_help(); - } else if (subCmd == "map") { -diff --git a/src/complementFile/complementFile.cpp b/src/complementFile/complementFile.cpp -index 803b7c5..5d3b384 100644 ---- a/src/complementFile/complementFile.cpp -+++ b/src/complementFile/complementFile.cpp -@@ -38,7 +38,7 @@ void ComplementFile::processHits(RecordOutputMgr *outputMgr, RecordKeyVector &hi - const Record *rec = hits.getKey(); - - //test for chrom change. -- const QuickString &newChrom = rec->getChrName(); -+ const string &newChrom = rec->getChrName(); - if (_currChrom != newChrom) { - - outPutLastRecordInPrevChrom(); -@@ -95,7 +95,7 @@ void ComplementFile::giveFinalReport(RecordOutputMgr *outputMgr) { - - void ComplementFile::outPutLastRecordInPrevChrom() - { -- const QuickString &chrom = _outRecord.getChrName(); -+ const string &chrom = _outRecord.getChrName(); - - //do nothing if triggered by first record in DB. At this point, - //there was no prev chrom, so nothing is stored in the output Record yet. -@@ -106,7 +106,7 @@ void ComplementFile::outPutLastRecordInPrevChrom() - printRecord(maxChromSize); - } - --bool ComplementFile::fastForward(const QuickString &newChrom) { -+bool ComplementFile::fastForward(const string &newChrom) { - if (!newChrom.empty() && !_genomeFile->hasChrom(newChrom)) return false; - - int i= _currPosInGenomeList +1; -@@ -133,14 +133,14 @@ bool ComplementFile::fastForward(const QuickString &newChrom) { - void ComplementFile::printRecord(int endPos) - { - _outRecord.setStartPos(_currStartPos); -- QuickString startStr; -- startStr.append(_currStartPos); -- _outRecord.setStartPosStr(startStr); -+ stringstream startStr; -+ startStr << _currStartPos; -+ _outRecord.setStartPosStr(startStr.str()); - - _outRecord.setEndPos(endPos); -- QuickString endStr; -- endStr.append(endPos); -- _outRecord.setEndPosStr(endStr); -+ stringstream endStr; -+ endStr << endPos; -+ _outRecord.setEndPosStr(endStr.str()); - - _outputMgr->printRecord(&_outRecord); - _outputMgr->newline(); -diff --git a/src/complementFile/complementFile.h b/src/complementFile/complementFile.h -index 3382dbd..a90b6c2 100644 ---- a/src/complementFile/complementFile.h -+++ b/src/complementFile/complementFile.h -@@ -34,17 +34,17 @@ public: - protected: - FileRecordMergeMgr *_frm; - Bed3Interval _outRecord; -- QuickString _currChrom; -+ string _currChrom; - const NewGenomeFile *_genomeFile; - int _currStartPos; - RecordOutputMgr *_outputMgr; -- const vector<QuickString> &_chromList; -+ const vector<string> &_chromList; - int _currPosInGenomeList; - - virtual ContextComplement *upCast(ContextBase *context) { return static_cast<ContextComplement *>(context); } - - void outPutLastRecordInPrevChrom(); -- bool fastForward(const QuickString &newChrom); -+ bool fastForward(const string &newChrom); - void printRecord(int endPos); - - }; -diff --git a/src/coverageFile/coverageFile.cpp b/src/coverageFile/coverageFile.cpp -index 9473eeb..b01eda4 100644 ---- a/src/coverageFile/coverageFile.cpp -+++ b/src/coverageFile/coverageFile.cpp -@@ -6,6 +6,7 @@ - */ - - #include "coverageFile.h" -+#include <iomanip> - - CoverageFile::CoverageFile(ContextCoverage *context) - : IntersectFile(context), -@@ -13,6 +14,7 @@ CoverageFile::CoverageFile(ContextCoverage *context) - _depthArrayCapacity(0), - _queryLen(0), - _totalQueryLen(0), -+ _hitCount(0), - _queryOffset(0), - _floatValBuf(NULL) - { -@@ -34,40 +36,38 @@ CoverageFile::~CoverageFile() { - } - - --void CoverageFile::processHits(RecordOutputMgr *outputMgr, RecordKeyVector &hits) { -- makeDepthCount(hits); -- _finalOutput.clear(); -- -- switch(upCast(_context)->getCoverageType()) { -- case ContextCoverage::COUNT: -- doCounts(outputMgr, hits); -- break; -- -- case ContextCoverage::PER_BASE: -- doPerBase(outputMgr, hits); -- break; -- -- case ContextCoverage::MEAN: -- doMean(outputMgr, hits); -- break; -- -- case ContextCoverage::HIST: -- doHist(outputMgr, hits); -- break; -- -- case ContextCoverage::DEFAULT: -- default: -- doDefault(outputMgr, hits); -- break; -- -- } -- -+void CoverageFile::processHits(RecordOutputMgr *outputMgr, RecordKeyVector &hits) -+{ -+ makeDepthCount(hits); -+ _finalOutput.clear(); -+ -+ switch(upCast(_context)->getCoverageType()) { -+ case ContextCoverage::COUNT: -+ doCounts(outputMgr, hits); -+ break; -+ -+ case ContextCoverage::PER_BASE: -+ doPerBase(outputMgr, hits); -+ break; -+ -+ case ContextCoverage::MEAN: -+ doMean(outputMgr, hits); -+ break; -+ -+ case ContextCoverage::HIST: -+ doHist(outputMgr, hits); -+ break; -+ -+ case ContextCoverage::DEFAULT: -+ default: -+ doDefault(outputMgr, hits); -+ break; -+ } - } - - void CoverageFile::cleanupHits(RecordKeyVector &hits) { - IntersectFile::cleanupHits(hits); - memset(_depthArray, 0, sizeof(size_t) * _queryLen); -- - } - - void CoverageFile::giveFinalReport(RecordOutputMgr *outputMgr) { -@@ -77,19 +77,25 @@ void CoverageFile::giveFinalReport(RecordOutputMgr *outputMgr) { - return; - } - -+ - for (depthMapType::iterator iter = _finalDepthMap.begin(); iter != _finalDepthMap.end(); iter++) { - size_t depth = iter->first; - size_t basesAtDepth = iter->second; -+ //cout << "x\n"; - float depthPct = (float)basesAtDepth / (float)_totalQueryLen; -- -- _finalOutput = "all\t"; -- _finalOutput.append(static_cast<uint32_t>(depth)); -- _finalOutput.append("\t"); -- _finalOutput.append(static_cast<uint32_t>(basesAtDepth)); -- _finalOutput.append("\t"); -- _finalOutput.append(static_cast<uint32_t>(_totalQueryLen)); -- _finalOutput.append("\t"); -- format(depthPct); -+ //cout << "y\n"; -+ ostringstream s; -+ s << "all\t"; -+ s << depth; -+ s << "\t"; -+ s << basesAtDepth; -+ s << "\t"; -+ s << _totalQueryLen; -+ s << "\t"; -+ char *depthPctString; -+ asprintf(&depthPctString, "%0.7f", depthPct); -+ s << depthPctString; -+ _finalOutput = s.str(); - - outputMgr->printRecord(NULL, _finalOutput); - } -@@ -101,24 +107,57 @@ void CoverageFile::makeDepthCount(RecordKeyVector &hits) { - _queryLen = (size_t)(key->getEndPos() - _queryOffset); - _totalQueryLen += _queryLen; - -- //resize depth array if needed -+ // resize depth array if needed - if (_depthArrayCapacity < _queryLen) { - _depthArray = (size_t*)realloc(_depthArray, sizeof(size_t) * _queryLen); - _depthArrayCapacity = _queryLen; - memset(_depthArray, 0, sizeof(size_t) * _depthArrayCapacity); - } -- -- //loop through hits, which may not be in sorted order, due to -- //potential multiple databases, and increment the depth array as needed. -- for (RecordKeyVector::const_iterator_type iter = hits.begin(); iter != hits.end(); iter = hits.next()) { -- const Record *dbRec = *iter; -- int dbStart = dbRec->getStartPos(); -- int dbEnd = dbRec->getEndPos(); -- int maxStart = max(_queryOffset, dbStart); -- int minEnd = min(dbEnd, key->getEndPos()); -- -- for (int i=maxStart; i < minEnd; i++) { -- _depthArray[i - _queryOffset]++; -+ _hitCount = 0; -+ // no -split -+ if (!(_context)->getObeySplits()) -+ { -+ //loop through hits, which may not be in sorted order, due to -+ //potential multiple databases, and increment the depth array as needed. -+ for (RecordKeyVector::iterator_type iter = hits.begin(); iter != hits.end(); iter = hits.next()) -+ { -+ const Record *dbRec = *iter; -+ int dbStart = dbRec->getStartPos(); -+ int dbEnd = dbRec->getEndPos(); -+ int maxStart = max(_queryOffset, dbStart); -+ int minEnd = min(dbEnd, key->getEndPos()); -+ -+ for (int i=maxStart; i < minEnd; i++) { -+ _depthArray[i - _queryOffset]++; -+ } -+ _hitCount++; -+ } -+ } -+ // -split -+ else -+ { -+ for (RecordKeyVector::iterator_type iter = hits.begin(); iter != hits.end(); iter = hits.next()) { -+ const Record *dbRec = *iter; -+ bool count_hit = false; -+ for (size_t i = 0; i < dbRec->block_starts.size(); ++i) -+ { -+ int block_start = dbRec->block_starts[i]; -+ int block_end = dbRec->block_ends[i]; -+ int maxStart = max(_queryOffset, block_start); -+ int minEnd = min(block_end, key->getEndPos()); -+ if ((minEnd - maxStart) > 0) -+ { -+ for (int i = maxStart; i < minEnd; i++) -+ { -+ _depthArray[i - _queryOffset]++; -+ } -+ count_hit = true; -+ } -+ } -+ if (count_hit) -+ { -+ _hitCount++; -+ } - } - } - } -@@ -135,19 +174,23 @@ size_t CoverageFile::countBasesAtDepth(size_t depth) { - - void CoverageFile::doCounts(RecordOutputMgr *outputMgr, RecordKeyVector &hits) - { -- _finalOutput = static_cast<uint32_t>(hits.size()); -+ ostringstream s; -+ s << _hitCount; -+ _finalOutput.append(s.str()); - outputMgr->printRecord(hits.getKey(), _finalOutput); - } - - void CoverageFile::doPerBase(RecordOutputMgr *outputMgr, RecordKeyVector &hits) - { - //loop through all bases in query, printing full record and metrics for each -- const Record * queryRec = hits.getKey(); -+ -+ Record * queryRec = hits.getKey(); - for (size_t i= 0; i < _queryLen; i++) { -- _finalOutput = static_cast<uint32_t>(i+1); -- _finalOutput.append("\t"); -- _finalOutput.append(static_cast<uint32_t>(_depthArray[i])); -- -+ ostringstream s; -+ s << (i+1); -+ s << "\t"; -+ s << _depthArray[i]; -+ _finalOutput = s.str(); - outputMgr->printRecord(queryRec, _finalOutput); - } - } -@@ -158,7 +201,12 @@ void CoverageFile::doMean(RecordOutputMgr *outputMgr, RecordKeyVector &hits) - for (size_t i= 0; i < _queryLen; i++) { - sum += _depthArray[i]; - } -- format((float)sum / (float)_queryLen); -+ ostringstream s; -+ float mean = ((float)sum / (float)_queryLen); -+ char *meanString; -+ asprintf(&meanString, "%0.7f", mean); -+ s << meanString; -+ _finalOutput.append(s.str()); - outputMgr->printRecord(hits.getKey(), _finalOutput); - } - -@@ -166,7 +214,6 @@ void CoverageFile::doMean(RecordOutputMgr *outputMgr, RecordKeyVector &hits) - void CoverageFile::doHist(RecordOutputMgr *outputMgr, RecordKeyVector &hits) - { - //make a map of depths to num bases with that depth -- - _currDepthMap.clear(); - for (size_t i=0; i < _queryLen; i++) { - _currDepthMap[_depthArray[i]]++; -@@ -176,40 +223,38 @@ void CoverageFile::doHist(RecordOutputMgr *outputMgr, RecordKeyVector &hits) - for (depthMapType::iterator iter = _currDepthMap.begin(); iter != _currDepthMap.end(); iter++) { - size_t depth = iter->first; - size_t numBasesAtDepth = iter->second; -- float coveredBases = (float)numBasesAtDepth / (float)_queryLen; -- -- _finalOutput = static_cast<uint32_t>(depth); -- _finalOutput.append("\t"); -- _finalOutput.append(static_cast<uint32_t>(numBasesAtDepth)); -- _finalOutput.append("\t"); -- _finalOutput.append(static_cast<uint32_t>(_queryLen)); -- _finalOutput.append("\t"); -- format(coveredBases); -- -+ float coveredFraction = (float)numBasesAtDepth / (float)_queryLen; -+ -+ ostringstream s; -+ s << depth; -+ s << "\t"; -+ s << numBasesAtDepth; -+ s << "\t"; -+ s << _queryLen; -+ s << "\t"; -+ char *coveredFractionString; -+ asprintf(&coveredFractionString, "%0.7f", coveredFraction); -+ s << coveredFractionString; -+ _finalOutput = s.str(); - outputMgr->printRecord(hits.getKey(), _finalOutput); - } -- - } - - void CoverageFile::doDefault(RecordOutputMgr *outputMgr, RecordKeyVector &hits) - { - size_t nonZeroBases = _queryLen - countBasesAtDepth(0); -- float coveredBases = (float)nonZeroBases / (float)_queryLen; -- -- _finalOutput = static_cast<uint32_t>(hits.size()); -- _finalOutput.append("\t"); -- _finalOutput.append(static_cast<uint32_t>(nonZeroBases)); -- _finalOutput.append("\t"); -- _finalOutput.append(static_cast<uint32_t>(_queryLen)); -- _finalOutput.append("\t"); -- format(coveredBases); -- -+ float coveredFraction = (float)nonZeroBases / (float)_queryLen; -+ -+ ostringstream s; -+ s << _hitCount; -+ s << "\t"; -+ s << nonZeroBases; -+ s << "\t"; -+ s << _queryLen; -+ s << "\t"; -+ char *coveredFractionString; -+ asprintf(&coveredFractionString, "%0.7f", coveredFraction); -+ s << coveredFractionString; -+ _finalOutput = s.str(); - outputMgr->printRecord(hits.getKey(), _finalOutput); - } -- --void CoverageFile::format(float val) --{ -- memset(_floatValBuf, 0, floatValBufLen); -- sprintf(_floatValBuf, "%0.7f", val); -- _finalOutput.append(_floatValBuf); --} -diff --git a/src/coverageFile/coverageFile.h b/src/coverageFile/coverageFile.h -index fa2c662..691b74f 100644 ---- a/src/coverageFile/coverageFile.h -+++ b/src/coverageFile/coverageFile.h -@@ -8,6 +8,7 @@ - #ifndef COVERAGEFILE_H_ - #define COVERAGEFILE_H_ - -+#include <stdio.h> // for asprintf - #include "intersectFile.h" - #include "ContextCoverage.h" - -@@ -21,12 +22,13 @@ public: - - - protected: -- QuickString _finalOutput; -+ string _finalOutput; - - size_t *_depthArray; - size_t _depthArrayCapacity; - size_t _queryLen; - size_t _totalQueryLen; -+ size_t _hitCount; - int _queryOffset; - static const int DEFAULT_DEPTH_CAPACITY = 1024; - char *_floatValBuf; -@@ -47,9 +49,6 @@ protected: - void doMean(RecordOutputMgr *outputMgr, RecordKeyVector &hits); - void doHist(RecordOutputMgr *outputMgr, RecordKeyVector &hits); - void doDefault(RecordOutputMgr *outputMgr, RecordKeyVector &hits); -- -- void format(float val); -- - }; - - -diff --git a/src/fisher/fisher.cpp b/src/fisher/fisher.cpp -index 7548f18..583b467 100644 ---- a/src/fisher/fisher.cpp -+++ b/src/fisher/fisher.cpp -@@ -91,7 +91,7 @@ void Fisher::giveFinalReport(RecordOutputMgr *outputMgr) - unsigned long Fisher::getTotalIntersection(RecordKeyVector &recList) - { - unsigned long intersection = 0; -- const Record *key = recList.getKey(); -+ Record *key = recList.getKey(); - int keyStart = key->getStartPos(); - int keyEnd = key->getEndPos(); - -@@ -99,7 +99,7 @@ unsigned long Fisher::getTotalIntersection(RecordKeyVector &recList) - _qsizes.push_back((keyEnd - keyStart)); - - int hitIdx = 0; -- for (RecordKeyVector::const_iterator_type iter = recList.begin(); iter != recList.end(); iter = recList.next()) { -+ for (RecordKeyVector::iterator_type iter = recList.begin(); iter != recList.end(); iter = recList.next()) { - int maxStart = max((*iter)->getStartPos(), keyStart); - int minEnd = min((*iter)->getEndPos(), keyEnd); - _qsizes.push_back((int)(minEnd - maxStart)); -diff --git a/src/groupBy/Makefile b/src/groupBy/Makefile -index 9bb141a..44cd7aa 100644 ---- a/src/groupBy/Makefile -+++ b/src/groupBy/Makefile -@@ -10,6 +10,7 @@ INCLUDES = -I$(UTILITIES_DIR)/Contexts/ \ - -I$(UTILITIES_DIR)/general/ \ - -I$(UTILITIES_DIR)/fileType/ \ - -I$(UTILITIES_DIR)/lineFileUtilities/ \ -+ -I$(UTILITIES_DIR)/stringUtilities/ \ - -I$(UTILITIES_DIR)/gzstream/ \ - -I$(UTILITIES_DIR)/GenomeFile/ \ - -I$(UTILITIES_DIR)/BamTools/include \ -diff --git a/src/groupBy/groupBy.cpp b/src/groupBy/groupBy.cpp -index 867f15f..1e1dbda 100644 ---- a/src/groupBy/groupBy.cpp -+++ b/src/groupBy/groupBy.cpp -@@ -7,6 +7,8 @@ - #include "groupBy.h" - #include "Tokenizer.h" - #include "ParseTools.h" -+#include "stringUtilities.h" -+#include <utility> - - GroupBy::GroupBy(ContextGroupBy *context) - : ToolBase(context), -@@ -29,8 +31,8 @@ bool GroupBy::init() - for (int i=0; i < numElems; i++) { - //if the item is a range, such as 3-5, - //must split that as well. -- const QuickString &elem = groupColsTokens.getElem(i); - -+ const string &elem = groupColsTokens.getElem(i); - if (strchr(elem.c_str(), '-')) { - Tokenizer rangeElems; - rangeElems.tokenize(elem, '-'); -@@ -59,14 +61,19 @@ bool GroupBy::findNext(RecordKeyVector &hits) - assignPrevFields(); - hits.setKey(_prevRecord); - hits.push_back(_prevRecord); //key should also be part of group for calculations -- while (1) { -- const Record *newRecord = getNextRecord(); -- if (newRecord == NULL) { -+ while (1) -+ { -+ Record *newRecord = getNextRecord(); -+ if (newRecord == NULL) -+ { - _prevRecord = NULL; - break; -- } else if (canGroup(newRecord)) { -+ } else if (canGroup(newRecord)) -+ { - hits.push_back(newRecord); -- } else { -+ } -+ else -+ { - _prevRecord = newRecord; - break; - } -@@ -77,15 +84,19 @@ bool GroupBy::findNext(RecordKeyVector &hits) - void GroupBy::processHits(RecordOutputMgr *outputMgr, RecordKeyVector &hits) - { - -- const Record *rec = hits.getKey(); -- const QuickString &opVal = _context->getColumnOpsVal(hits); -- if (upCast(_context)->printFullCols()) { -+ Record *rec = hits.getKey(); -+ const string &opVal = _context->getColumnOpsVal(hits); -+ if (upCast(_context)->printFullCols()) -+ { - outputMgr->printRecord(rec, opVal); -- } else { -- QuickString outBuf; -- for (int i=0; i < (int)_groupCols.size(); i++) { -+ } -+ else -+ { -+ string outBuf; -+ for (int i = 0; i < (int)_groupCols.size(); i++) -+ { - outBuf.append(rec->getField(_groupCols[i])); -- outBuf.append('\t'); -+ outBuf.append("\t"); - } - outBuf.append(opVal); - outputMgr->printRecord(NULL, outBuf); -@@ -95,7 +106,7 @@ void GroupBy::processHits(RecordOutputMgr *outputMgr, RecordKeyVector &hits) - - void GroupBy::cleanupHits(RecordKeyVector &hits) - { -- RecordKeyVector::const_iterator_type iter = hits.begin(); -+ RecordKeyVector::iterator_type iter = hits.begin(); - for (; iter != hits.end(); iter = hits.next()) - { - _queryFRM->deleteRecord(*iter); -@@ -103,12 +114,16 @@ void GroupBy::cleanupHits(RecordKeyVector &hits) - hits.clearAll(); - } - --const Record *GroupBy::getNextRecord() { -- while (!_queryFRM->eof()) { -+Record *GroupBy::getNextRecord() { -+ while (!_queryFRM->eof()) -+ { - Record *queryRecord = _queryFRM->getNextRecord(); -- if (queryRecord == NULL) { -+ if (queryRecord == NULL) -+ { - continue; -- } else { -+ } -+ else -+ { - return queryRecord; - } - } -@@ -121,19 +136,22 @@ void GroupBy::assignPrevFields() { - } - } - --bool GroupBy::canGroup(const Record *newRecord) { -- -- for (int i=0; i < (int)_groupCols.size(); i++) { -+bool GroupBy::canGroup(Record *newRecord) -+{ -+ for (int i = 0; i < (int)_groupCols.size(); i++) -+ { - int fieldNum = _groupCols[i]; -- const QuickString &newField = newRecord->getField(fieldNum); -- const QuickString &oldField = _prevFields[i]; -- if (upCast(_context)->ignoreCase()) { -- if (oldField.stricmp(newField)) return false; -- } else { -+ const string &newField = newRecord->getField(fieldNum); -+ const string &oldField = _prevFields[i]; -+ if (upCast(_context)->ignoreCase()) -+ { -+ if (toLower(oldField) != toLower(newField)) return false; -+ } -+ else -+ { - if (oldField != newField) return false; - } - } - return true; -- - } - -diff --git a/src/groupBy/groupBy.h b/src/groupBy/groupBy.h -index 2c96dc9..c44ba3c 100644 ---- a/src/groupBy/groupBy.h -+++ b/src/groupBy/groupBy.h -@@ -27,11 +27,11 @@ protected: - virtual ContextGroupBy *upCast(ContextBase *context) { return static_cast<ContextGroupBy *>(context); } - - vector<int> _groupCols; -- vector<QuickString> _prevFields; -+ vector<string> _prevFields; - FileRecordMgr *_queryFRM; -- const Record *_prevRecord; -- const Record *getNextRecord(); -- bool canGroup(const Record *); -+ Record *_prevRecord; -+ Record *getNextRecord(); -+ bool canGroup(Record *); - void assignPrevFields(); - }; - -diff --git a/src/intersectFile/intersectFile.cpp b/src/intersectFile/intersectFile.cpp -index 01bb222..45977fc 100644 ---- a/src/intersectFile/intersectFile.cpp -+++ b/src/intersectFile/intersectFile.cpp -@@ -67,6 +67,7 @@ bool IntersectFile::findNext(RecordKeyVector &hits) - - void IntersectFile::processHits(RecordOutputMgr *outputMgr, RecordKeyVector &hits) - { -+ RecordKeyVector::iterator_type hitListIter = hits.begin(); - outputMgr->printRecord(hits); - } - -@@ -120,19 +121,16 @@ void IntersectFile::makeSweep() { - void IntersectFile::checkSplits(RecordKeyVector &hitSet) - { - if (upCast(_context)->getObeySplits()) { -- RecordKeyVector keySet(hitSet.getKey()); -- RecordKeyVector resultSet(hitSet.getKey()); -- RecordKeyVector overlapSet(hitSet.getKey()); -- upCast(_context)->getSplitBlockInfo()->findBlockedOverlaps(keySet, hitSet, resultSet, overlapSet); -- -+ - // when using coverage, we need a list of the sub-intervals of coverage - // so that per-base depth can be properly calculated when obeying splits - if (_context->getProgram() == ContextBase::COVERAGE) - { -- hitSet.swap(overlapSet); -+ upCast(_context)->getSplitBlockInfo()->findBlockedOverlaps(hitSet, true); - } -- else { -- hitSet.swap(resultSet); -+ else -+ { -+ upCast(_context)->getSplitBlockInfo()->findBlockedOverlaps(hitSet, false); - } - } - } -diff --git a/src/intersectFile/intersectFile.h b/src/intersectFile/intersectFile.h -index f40e750..3c85f93 100644 ---- a/src/intersectFile/intersectFile.h -+++ b/src/intersectFile/intersectFile.h -@@ -26,11 +26,11 @@ public: - IntersectFile(ContextIntersect *context); - virtual ~IntersectFile(); - virtual bool init(); -- virtual bool findNext(RecordKeyVector &hits); -- virtual void processHits(RecordOutputMgr *outputMgr, RecordKeyVector &hits); -- virtual void cleanupHits(RecordKeyVector &hits); -+ virtual bool findNext(RecordKeyVector &); -+ virtual void processHits(RecordOutputMgr *, RecordKeyVector &); -+ virtual void cleanupHits(RecordKeyVector &); - virtual bool finalizeCalculations(); -- virtual void giveFinalReport(RecordOutputMgr *outputMgr) {} -+ virtual void giveFinalReport(RecordOutputMgr *) {} - - - protected: -diff --git a/src/jaccard/jaccard.cpp b/src/jaccard/jaccard.cpp -index c99c117..2f61b86 100644 ---- a/src/jaccard/jaccard.cpp -+++ b/src/jaccard/jaccard.cpp -@@ -57,13 +57,13 @@ void Jaccard::giveFinalReport(RecordOutputMgr *outputMgr) { - unsigned long Jaccard::getTotalIntersection(RecordKeyVector &hits) - { - unsigned long intersection = 0; -- const Record *key = hits.getKey(); -+ Record *key = hits.getKey(); - int keyStart = key->getStartPos(); - int keyEnd = key->getEndPos(); - - int hitIdx = 0; -- for (RecordKeyVector::const_iterator_type iter = hits.begin(); iter != hits.end(); iter = hits.next()) { -- const Record *currRec = *iter; -+ for (RecordKeyVector::iterator_type iter = hits.begin(); iter != hits.end(); iter = hits.next()) { -+ Record *currRec = *iter; - int maxStart = max(currRec->getStartPos(), keyStart); - int minEnd = min(currRec->getEndPos(), keyEnd); - if (_context->getObeySplits()) { -diff --git a/src/jaccard/jaccard.h b/src/jaccard/jaccard.h -index e23ad9c..8c4f6db 100644 ---- a/src/jaccard/jaccard.h -+++ b/src/jaccard/jaccard.h -@@ -15,11 +15,11 @@ class Jaccard : public IntersectFile { - - public: - Jaccard(ContextJaccard *context); -- virtual bool findNext(RecordKeyVector &hits); -- virtual void processHits(RecordOutputMgr *outputMgr, RecordKeyVector &hits) {} -- virtual void cleanupHits(RecordKeyVector &hits); -+ virtual bool findNext(RecordKeyVector &); -+ virtual void processHits(RecordOutputMgr *, RecordKeyVector &) {} -+ virtual void cleanupHits(RecordKeyVector &); - virtual bool finalizeCalculations(); -- virtual void giveFinalReport(RecordOutputMgr *outputMgr); -+ virtual void giveFinalReport(RecordOutputMgr *); - - - protected: -diff --git a/src/nekSandbox1/nekSandboxMain.cpp b/src/nekSandbox1/nekSandboxMain.cpp -index d228540..d9b298a 100644 ---- a/src/nekSandbox1/nekSandboxMain.cpp -+++ b/src/nekSandbox1/nekSandboxMain.cpp -@@ -67,7 +67,7 @@ int nek_sandbox1_main(int argc,char** argv) - // printf("%s", sLine); - // } - // return 0; --// QuickString filename(argv[1]); -+// string filename(argv[1]); - // istream *inputStream = NULL; - // if (filename == "-") { - // inputStream = &cin; -@@ -91,7 +91,7 @@ int nek_sandbox1_main(int argc,char** argv) - //// exit(1); - //// } - //// } --// QuickString _bamHeader = _bamReader.GetHeaderText(); -+// string _bamHeader = _bamReader.GetHeaderText(); - // BamTools::RefVector _references = _bamReader.GetReferenceData(); - // - // if (_bamHeader.empty() || _references.empty()) { -@@ -107,10 +107,10 @@ int nek_sandbox1_main(int argc,char** argv) - // exit(1); - // } - // string sLine; --// vector<QuickString> fields; --// QuickString chrName; -+// vector<string> fields; -+// string chrName; - // --// vector<QuickString> chroms; -+// vector<string> chroms; - // chroms.push_back("1"); - // chroms.push_back("2"); - // chroms.push_back("10"); -@@ -127,7 +127,7 @@ int nek_sandbox1_main(int argc,char** argv) - // continue; - // } - // Tokenize(sLine.c_str(), fields); --// const QuickString &currChrom = fields[2]; -+// const string &currChrom = fields[2]; - // if (currChrom == chroms[chromIdx]) { - // cout << sLine << endl; - // chromCounts[chromIdx]++; -@@ -157,7 +157,7 @@ int nek_sandbox1_main(int argc,char** argv) - // cout << "RecordType is : " << frm.getRecordType() << ", " << frm.getRecordTypeName() << "." << endl; - // - // bool headerFound = false; --// QuickString outbuf; -+// string outbuf; - // while (!frm.eof()) { - // Record *record = frm.getNextRecord(); - // if (!headerFound && frm.hasHeader()) { -diff --git a/src/regressTest/regressTestMain.cpp b/src/regressTest/regressTestMain.cpp -index 0377ca6..01a2816 100644 ---- a/src/regressTest/regressTestMain.cpp -+++ b/src/regressTest/regressTestMain.cpp -@@ -3,7 +3,7 @@ - #include <cstring> - #include <cstdlib> - #include <cstdio> --#include "QuickString.h" -+#include "string.h" - - void usage() { - printf("Usage: bedtools regressTest sub-prog targetVersion configFile [optionsToTest]\n"); -@@ -31,7 +31,7 @@ int regress_test_main(int argc, char **argv) { - usage(); - exit(1); - } -- QuickString program(argv[2]); -+ string program(argv[2]); - - RegressTest *regressTest = new RegressTest(); - -diff --git a/src/shiftBed/shiftBed.cpp b/src/shiftBed/shiftBed.cpp -index 81022f8..50724ce 100644 ---- a/src/shiftBed/shiftBed.cpp -+++ b/src/shiftBed/shiftBed.cpp -@@ -51,7 +51,7 @@ void BedShift::AddShift(BED &bed) { ... 5796 lines suppressed ... -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/bedtools.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
