map uses PFM.

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);
-        }
-    }
 }
-*/

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);
 
 };

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;