[med-svn] [bedtools] 04/05: Refresh patches
Andreas Tille
tille at debian.org
Sat Feb 10 08:58:03 UTC 2018
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository bedtools.
commit b98c0172a28e89f2ecaeddcbddfcc6b927590ca5
Author: Andreas Tille <tille at debian.org>
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 <tille at debian.org>
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 ...
--
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