diff --git a/src/mapFile/mapFile.cpp b/src/mapFile/mapFile.cpp
index 360b6d69697713b770b7951bfd1dfe55bf15e648..3bd133d2b4fb13c01d58eecaa97dd9e48e091a37 100644
--- a/src/mapFile/mapFile.cpp
+++ b/src/mapFile/mapFile.cpp
@@ -55,187 +55,70 @@ bool FileMap::mapFiles()
//} else {
//}
//_recordOutputMgr->printKeyAndTerminate(hitSet);
- _recordOutputMgr->printRecord(hitSet.getKey(), MapHits(hitSet));
+ SummarizeHits(hitSet);
+ _recordOutputMgr->printRecord(hitSet.getKey(), _output);
}
return true;
}
void FileMap::ExtractColumnFromHits(RecordKeyList &hits) {
- for (RecordKeyList::const_iterator_type iter = hits.begin(); iter != hits.end(); iter = hits.next()) {
- try {
- ostringstream startString;
- startString << iter->value()->getStartPos();
- //_column_vec.push_back(iter->value().fields.at(_column));
- _column_vec.push_back(startString.str());
- }
- catch(std::out_of_range& e) {
- exit(1);
- }
- /*
- catch(std::out_of_range& e) {
- cerr << endl << "*****" << endl
- << "*****ERROR: requested column ("
- << _column + 1
- << ") exceeds the number of columns in file at line "
- << _bedA->_lineNum << ". Exiting."
- << endl << "*****" << endl;
- exit(1);
- }
- */
+ _column_vec.clear();
+ RecordKeyList::const_iterator_type iter = hits.begin();
+ for (; iter != hits.end(); iter = hits.next())
+ {
+ _column_vec.push_back(iter->value()->getField(_context->getColumn()).str());
}
-}
+}
-string FileMap::MapHits(RecordKeyList &hits) {
-
- ostringstream output;
- if (hits.size() == 0)
- // FIX ME
- return "-1";
- //return _nullValue;
+void FileMap::SummarizeHits(RecordKeyList &hits) {
- ExtractColumnFromHits(hits);
+ const QuickString & operation = _context->getColumnOperation();
+ _output.clear();
+
+ if (hits.size() == 0) {
+ if (operation == "count" || operation == "count_distinct")
+ _output.append("0");
+ else
+ _output.append(_context->getNullValue().str());
+ return;
+ }
- string operation = _context->getColumnOperation();
+ _tmp_output.str("");
+ _tmp_output.clear();
+
+ ExtractColumnFromHits(hits);
VectorOps vo(_column_vec);
if (operation == "sum")
- output << setprecision (PRECISION) << vo.GetSum();
+ _tmp_output << setprecision (PRECISION) << vo.GetSum();
else if (operation == "mean")
- output << setprecision (PRECISION) << vo.GetMean();
+ _tmp_output << setprecision (PRECISION) << vo.GetMean();
else if (operation == "median")
- output << setprecision (PRECISION) << vo.GetMedian();
+ _tmp_output << setprecision (PRECISION) << vo.GetMedian();
else if (operation == "min")
- output << setprecision (PRECISION) << vo.GetMin();
+ _tmp_output << setprecision (PRECISION) << vo.GetMin();
else if (operation == "max")
- output << setprecision (PRECISION) << vo.GetMax();
+ _tmp_output << setprecision (PRECISION) << vo.GetMax();
+ else if (operation == "absmin")
+ _tmp_output << setprecision (PRECISION) << vo.GetAbsMin();
+ else if (operation == "absmax")
+ _tmp_output << setprecision (PRECISION) << vo.GetAbsMax();
else if (operation == "mode")
- output << vo.GetMode();
+ _tmp_output << vo.GetMode();
else if (operation == "antimode")
- output << vo.GetAntiMode();
+ _tmp_output << vo.GetAntiMode();
else if (operation == "count")
- output << setprecision (PRECISION) << vo.GetCount();
+ _tmp_output << setprecision (PRECISION) << vo.GetCount();
else if (operation == "count_distinct")
- output << setprecision (PRECISION) << vo.GetCountDistinct();
+ _tmp_output << setprecision (PRECISION) << vo.GetCountDistinct();
else if (operation == "collapse")
- output << vo.GetCollapse();
+ _tmp_output << vo.GetCollapse();
else if (operation == "distinct")
- output << vo.GetDistinct();
+ _tmp_output << vo.GetDistinct();
else {
cerr << "ERROR: " << operation << " is an unrecoginzed operation\n";
exit(1);
}
- _column_vec.clear();
- return output.str();
-}
-
-
-/*
-const int PRECISION = 21;
-double GetUserColumn(const string s);
-
-// Constructor
-BedMap::BedMap(string bedAFile, string bedBFile, int column, string operation,
- float overlapFraction, bool sameStrand,
- bool diffStrand, bool reciprocal,
- bool choseNullValue, string nullValue,
- bool printHeader)
-{
-
- _bedAFile = bedAFile;
- _bedBFile = bedBFile;
- _column = column - 1; // user's request is 1-based
- _operation = operation;
- _overlapFraction = overlapFraction;
- _sameStrand = sameStrand;
- _diffStrand = diffStrand;
- _reciprocal = reciprocal;
- _nullValue = nullValue;
- _printHeader = printHeader;
-
- if (!choseNullValue && operation == "count")
- _nullValue = "0";
- Map();
-}
-
-// Destructor
-BedMap::~BedMap(void)
-{}
-
-void BedMap::Map() {
+ _output.append(_tmp_output.str());
- // create new BED file objects for A and B
- _bedA = new BedFile(_bedAFile);
- _bedB = new BedFile(_bedBFile);
-
- // use the chromsweep algorithm to detect overlaps on the fly.
- ChromSweep sweep = ChromSweep(_bedA, _bedB,
- _sameStrand, _diffStrand,
- _overlapFraction, _reciprocal,
- false, _printHeader);
-
- pair<BED, vector<BED> > hit_set;
- hit_set.second.reserve(10000);
- while (sweep.Next(hit_set)) {
- string result = MapHits(hit_set.first, hit_set.second);
- _bedA->reportBedTab(hit_set.first);
- printf("%s\n", result.c_str());
- }
-}
-
-
-string BedMap::MapHits(const BED &a, const vector<BED> &hits) {
-
- ostringstream output;
- if (hits.size() == 0)
- return _nullValue;
-
- ExtractColumnFromHits(hits);
- VectorOps vo(_column_vec);
- if (_operation == "sum")
- output << setprecision (PRECISION) << vo.GetSum();
- else if (_operation == "mean")
- output << setprecision (PRECISION) << vo.GetMean();
- else if (_operation == "median")
- output << setprecision (PRECISION) << vo.GetMedian();
- else if (_operation == "min")
- output << setprecision (PRECISION) << vo.GetMin();
- else if (_operation == "max")
- output << setprecision (PRECISION) << vo.GetMax();
- else if (_operation == "mode")
- output << vo.GetMode();
- else if (_operation == "antimode")
- output << vo.GetAntiMode();
- else if (_operation == "count")
- output << setprecision (PRECISION) << vo.GetCount();
- else if (_operation == "count_distinct")
- output << setprecision (PRECISION) << vo.GetCountDistinct();
- else if (_operation == "collapse")
- output << vo.GetCollapse();
- else if (_operation == "distinct")
- output << vo.GetDistinct();
- else {
- cerr << "ERROR: " << _operation << " is an unrecoginzed operation\n";
- exit(1);
- }
- _column_vec.clear();
- return output.str();
-}
-
-
-void BedMap::ExtractColumnFromHits(const vector<BED> &hits) {
- for (size_t i = 0; i < hits.size(); ++i) {
- try {
- _column_vec.push_back(hits[i].fields.at(_column));
- }
- catch(std::out_of_range& e) {
- cerr << endl << "*****" << endl
- << "*****ERROR: requested column ("
- << _column + 1
- << ") exceeds the number of columns in file at line "
- << _bedA->_lineNum << ". Exiting."
- << endl << "*****" << endl;
- exit(1);
- }
- }
}
-*/
diff --git a/src/mapFile/mapFile.h b/src/mapFile/mapFile.h
index 57e97556ceacdb41541a3e97a7fb20e667fa2d17..cb1da082182baec7a78fd12b480ef684fee57701 100644
--- a/src/mapFile/mapFile.h
+++ b/src/mapFile/mapFile.h
@@ -42,11 +42,13 @@ private:
vector<string> _column_vec; // vector to hold current column's worth of data
+ ostringstream _tmp_output;
+ QuickString _output; // placeholder for the results of mapping B to each a in A.
//------------------------------------------------
// private methods
//------------------------------------------------
void Map();
- string MapHits(RecordKeyList &hits);
+ void SummarizeHits(RecordKeyList &hits);
void ExtractColumnFromHits(RecordKeyList &hits);
};
diff --git a/src/mapFile/mapMain.cpp b/src/mapFile/mapMain.cpp
index bc437edb25380782bf39b58ad4e2323ed18213f3..fe87c9f3d96cc6b1b98b69607f6a40affab05597 100644
--- a/src/mapFile/mapMain.cpp
+++ b/src/mapFile/mapMain.cpp
@@ -191,7 +191,7 @@ void map_help(void) {
cerr << "\t-o\t" << "Specify the operation that should be applied to -c." << endl;
cerr << "\t\t Valid operations:" << endl;
- cerr << "\t\t sum, min, max," << endl;
+ cerr << "\t\t sum, min, max, absmin, absmax," << endl;
cerr << "\t\t mean, median," << endl;
cerr << "\t\t collapse (i.e., print a comma separated list (duplicates allowed)), " << endl;
cerr << "\t\t distinct (i.e., print a comma separated list (NO duplicates allowed)), " << endl;
@@ -215,6 +215,9 @@ void map_help(void) {
cerr << "\t\tthat overlap A on the _opposite_ strand." << endl;
cerr << "\t\t- By default, overlaps are reported without respect to strand." << endl << endl;
+ cerr << "\t-g\t" << "Provide a genome file to enforce consistent chromosome sort order" << endl;
+ cerr <<"\t\tacross input files." << endl << endl;
+
cerr << "\t-null\t" << "The value to print if no overlaps are found for an A interval." << endl;
cerr << "\t\t- Default - \".\"" << endl << endl;