diff --git a/src/intersectFile/Makefile b/src/intersectFile/Makefile
index e265b3348d1b1883c8f46e15b2902e3f2e5f8933..8c81049e431a1fbb94ec92be94593c9c1ca3470d 100644
--- a/src/intersectFile/Makefile
+++ b/src/intersectFile/Makefile
@@ -17,6 +17,7 @@ INCLUDES = -I$(UTILITIES_DIR)/Contexts/ \
-I$(UTILITIES_DIR)/FileRecordTools/ \
-I$(UTILITIES_DIR)/FileRecordTools/FileReaders/ \
-I$(UTILITIES_DIR)/FileRecordTools/Records/ \
+ -I$(UTILITIES_DIR)/KeyListOps/ \
-I$(UTILITIES_DIR)/RecordOutputMgr/ \
-I$(UTILITIES_DIR)/NewChromsweep \
-I$(UTILITIES_DIR)/BinTree \
diff --git a/src/mapFile/mapFile.cpp b/src/mapFile/mapFile.cpp
index 7cff53109b6fff4d5184deb117d8a879ad39cf82..8dbf24ad54a2e93715fd453092e778efcdf24b0c 100644
--- a/src/mapFile/mapFile.cpp
+++ b/src/mapFile/mapFile.cpp
@@ -21,14 +21,11 @@ const int PRECISION = 21;
FileMap::FileMap(ContextMap *context)
: _context(context),
_blockMgr(NULL),
- _recordOutputMgr(NULL),
- _colOps(_context->getColOps())
+ _recordOutputMgr(NULL)
{
_blockMgr = new BlockMgr(_context->getOverlapFraction(), _context->getReciprocal());
_recordOutputMgr = new RecordOutputMgr();
_recordOutputMgr->init(_context);
- _keyListOps.setNullValue(_context->getNullValue());
- _keyListOps.setDelimStr(_context->getDelim());
}
FileMap::~FileMap(void) {
@@ -46,174 +43,15 @@ bool FileMap::mapFiles()
}
RecordKeyList hitSet;
while (sweep.next(hitSet)) {
- _outputValues.clear();
if (_context->getObeySplits()) {
RecordKeyList keySet(hitSet.getKey());
RecordKeyList resultSet(hitSet.getKey());
_blockMgr->findBlockedOverlaps(keySet, hitSet, resultSet);
- calculateOutput(resultSet);
- _recordOutputMgr->printRecord(resultSet.getKey(), _outputValues);
+ _recordOutputMgr->printRecord(resultSet.getKey(), _context->getColumnOpsVal(resultSet));
} else {
- calculateOutput(hitSet);
- _recordOutputMgr->printRecord(hitSet.getKey(), _outputValues);
+ _recordOutputMgr->printRecord(hitSet.getKey(), _context->getColumnOpsVal(hitSet));
}
}
return true;
}
-void FileMap::calculateOutput(RecordKeyList &hits)
-{
- //loop through all requested columns, and for each one, call the method needed
- //for the operation specified.
- _keyListOps.setKeyList(&hits);
-
- double val = 0.0;
- for (int i=0; i < (int)_colOps.size(); i++) {
- int col = _colOps[i].first;
- KeyListOps::OP_TYPES opCode = _colOps[i].second;
-
- _keyListOps.setColumn(col);
- switch (opCode) {
- case KeyListOps::SUM:
- val = _keyListOps.getSum();
- if (isnan(val)) {
- _outputValues.append(_context->getNullValue());
- } else {
- _outputValues.append(val);
- }
- break;
-
- case KeyListOps::MEAN:
- val = _keyListOps.getMean();
- if (isnan(val)) {
- _outputValues.append(_context->getNullValue());
- } else {
- _outputValues.append(val);
- }
- break;
-
- case KeyListOps::STDDEV:
- val = _keyListOps.getStddev();
- if (isnan(val)) {
- _outputValues.append(_context->getNullValue());
- } else {
- _outputValues.append(val);
- }
- break;
-
- case KeyListOps::SAMPLE_STDDEV:
- val = _keyListOps.getSampleStddev();
- if (isnan(val)) {
- _outputValues.append(_context->getNullValue());
- } else {
- _outputValues.append(val);
- }
- break;
-
- case KeyListOps::MEDIAN:
- val = _keyListOps.getMedian();
- if (isnan(val)) {
- _outputValues.append(_context->getNullValue());
- } else {
- _outputValues.append(val);
- }
- break;
-
- case KeyListOps::MODE:
- _outputValues.append(_keyListOps.getMode());
- break;
-
- case KeyListOps::ANTIMODE:
- _outputValues.append(_keyListOps.getAntiMode());
- break;
-
- case KeyListOps::MIN:
- val = _keyListOps.getMin();
- if (isnan(val)) {
- _outputValues.append(_context->getNullValue());
- } else {
- _outputValues.append(val);
- }
- break;
-
- case KeyListOps::MAX:
- val = _keyListOps.getMax();
- if (isnan(val)) {
- _outputValues.append(_context->getNullValue());
- } else {
- _outputValues.append(val);
- }
- break;
-
- case KeyListOps::ABSMIN:
- val = _keyListOps.getAbsMin();
- if (isnan(val)) {
- _outputValues.append(_context->getNullValue());
- } else {
- _outputValues.append(val);
- }
- break;
-
- case KeyListOps::ABSMAX:
- val = _keyListOps.getAbsMax();
- if (isnan(val)) {
- _outputValues.append(_context->getNullValue());
- } else {
- _outputValues.append(val);
- }
- break;
-
- case KeyListOps::COUNT:
- _outputValues.append(_keyListOps.getCount());
- break;
-
- case KeyListOps::DISTINCT:
- _outputValues.append(_keyListOps.getDistinct());
- break;
-
- case KeyListOps::COUNT_DISTINCT:
- _outputValues.append(_keyListOps.getCountDistinct());
- break;
-
- case KeyListOps::DISTINCT_ONLY:
- _outputValues.append(_keyListOps.getDistinctOnly());
- break;
-
- case KeyListOps::COLLAPSE:
- _outputValues.append(_keyListOps.getCollapse());
- break;
-
- case KeyListOps::CONCAT:
- _outputValues.append(_keyListOps.getConcat());
- break;
-
- case KeyListOps::FREQ_ASC:
- _outputValues.append(_keyListOps.getFreqAsc());
- break;
-
- case KeyListOps::FREQ_DESC:
- _outputValues.append(_keyListOps.getFreqDesc());
- break;
-
- case KeyListOps::FIRST:
- _outputValues.append(_keyListOps.getFirst());
- break;
-
- case KeyListOps::LAST:
- _outputValues.append(_keyListOps.getLast());
- break;
-
- case KeyListOps::INVALID:
- default:
- // Any unrecognized operation should have been handled already in the context validation.
- // It's thus unnecessary to handle it here, but throw an error to help us know if future
- // refactoring or code changes accidentally bypass the validation phase.
- cerr << "ERROR: Invalid operation given for column " << col << ". Exiting..." << endl;
- break;
- }
- //if this isn't the last column, add a tab.
- if (i < (int)_colOps.size() -1) {
- _outputValues.append('\t');
- }
- }
-}
diff --git a/src/mapFile/mapFile.h b/src/mapFile/mapFile.h
index e2143ef0fb110c2bb3fbde3500b3a5ee25403826..fbb431ac930bf68d7475f03ac8850438dd6d8302 100644
--- a/src/mapFile/mapFile.h
+++ b/src/mapFile/mapFile.h
@@ -38,11 +38,6 @@ private:
ContextMap *_context;
BlockMgr *_blockMgr;
RecordOutputMgr *_recordOutputMgr;
- KeyListOps _keyListOps;
- const ContextMap::colOpsType & _colOps;
- QuickString _outputValues; // placeholder for the results of mapping B to each a in A.
-
- void calculateOutput(RecordKeyList &hits);
};
#endif /* MAPFILE_H */
diff --git a/src/nekSandbox1/Makefile b/src/nekSandbox1/Makefile
index fbe6d8616676f86a02102b981f1d4e5c897ebf71..df8aba7262492b13bb9b9636577d01afa77d55ba 100644
--- a/src/nekSandbox1/Makefile
+++ b/src/nekSandbox1/Makefile
@@ -10,6 +10,7 @@ INCLUDES = -I$(UTILITIES_DIR)/Contexts/ \
-I$(UTILITIES_DIR)/FileRecordTools/ \
-I$(UTILITIES_DIR)/FileRecordTools/FileReaders \
-I$(UTILITIES_DIR)/FileRecordTools/Records \
+ -I$(UTILITIES_DIR)/KeyListOps/ \
-I$(UTILITIES_DIR)/general \
-I$(UTILITIES_DIR)/NewChromsweep \
-I$(UTILITIES_DIR)/GenomeFile/ \
diff --git a/src/regressTest/Makefile b/src/regressTest/Makefile
index e9ceebf3a43bc67ff0f1672139b174d66fb1f037..8ffeeab244a81930b3cf6cbe6bfbe62ece72bcaa 100644
--- a/src/regressTest/Makefile
+++ b/src/regressTest/Makefile
@@ -18,6 +18,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
-I$(UTILITIES_DIR)/FileRecordTools/ \
-I$(UTILITIES_DIR)/FileRecordTools/FileReaders \
-I$(UTILITIES_DIR)/FileRecordTools/Records \
+ -I$(UTILITIES_DIR)/KeyListOps/ \
-I$(UTILITIES_DIR)/general
# ----------------------------------
diff --git a/src/sampleFile/Makefile b/src/sampleFile/Makefile
index 2042291e68735b4316062d64a04e7f35d9847b2a..9ccbe5a9ef96b7ef4ed2d424fbc396794f2efc6c 100644
--- a/src/sampleFile/Makefile
+++ b/src/sampleFile/Makefile
@@ -17,6 +17,7 @@ INCLUDES = -I$(UTILITIES_DIR)/Contexts/ \
-I$(UTILITIES_DIR)/FileRecordTools/ \
-I$(UTILITIES_DIR)/FileRecordTools/FileReaders/ \
-I$(UTILITIES_DIR)/FileRecordTools/Records/ \
+ -I$(UTILITIES_DIR)/KeyListOps/ \
-I$(UTILITIES_DIR)/RecordOutputMgr/ \
-I$(UTILITIES_DIR)/version/
diff --git a/src/utils/BinTree/Makefile b/src/utils/BinTree/Makefile
index de04c816782689fc36ab33275d89bfa8f8d2a61e..c29b5ebadf2788b012c46e67330504e2edb52416 100644
--- a/src/utils/BinTree/Makefile
+++ b/src/utils/BinTree/Makefile
@@ -11,6 +11,7 @@ INCLUDES = -I$(UTILITIES_DIR)/general/ \
-I$(UTILITIES_DIR)/FileRecordTools/ \
-I$(UTILITIES_DIR)/FileRecordTools/FileReaders/ \
-I$(UTILITIES_DIR)/FileRecordTools/Records/ \
+ -I$(UTILITIES_DIR)/KeyListOps/ \
-I$(UTILITIES_DIR)/BamTools/include \
-I$(UTILITIES_DIR)/BamTools/src/ \
-I$(UTILITIES_DIR)/version/
diff --git a/src/utils/Contexts/ContextBase.cpp b/src/utils/Contexts/ContextBase.cpp
index 1f0c7a172e9d7af67377176dc400766bba43e276..adbc47afb4105c611661fa95c11a72aa990c25ed 100644
--- a/src/utils/Contexts/ContextBase.cpp
+++ b/src/utils/Contexts/ContextBase.cpp
@@ -52,11 +52,16 @@ ContextBase::ContextBase()
_hasConstantSeed(false),
_seed(0),
_forwardOnly(false),
- _reverseOnly(false)
+ _reverseOnly(false),
+ _hasColumnOpsMethods(false)
{
_programNames["intersect"] = INTERSECT;
_programNames["sample"] = SAMPLE;
_programNames["map"] = MAP;
+
+ if (hasColumnOpsMethods()) {
+ _keyListOps = new KeyListOps();
+ }
}
ContextBase::~ContextBase()
@@ -70,6 +75,11 @@ ContextBase::~ContextBase()
delete _files[i];
_files[i] = NULL;
}
+ if (hasColumnOpsMethods()) {
+ delete _keyListOps;
+ _keyListOps = NULL;
+ }
+
}
bool ContextBase::determineOutputType() {
@@ -167,6 +177,19 @@ bool ContextBase::parseCmdArgs(int argc, char **argv, int skipFirstArgs) {
else if (strcmp(_argv[_i], "-seed") == 0) {
if (!handle_seed()) return false;
}
+ else if (strcmp(_argv[_i], "-o") == 0) {
+ if (!handle_o()) return false;
+ }
+ else if (strcmp(_argv[_i], "-c") == 0) {
+ if (!handle_c()) return false;
+ }
+ else if (strcmp(_argv[_i], "-null") == 0) {
+ if (!handle_null()) return false;
+ }
+ else if (strcmp(_argv[_i], "-delim") == 0) {
+ if (!handle_delim()) return false;
+ }
+
}
return true;
}
@@ -182,6 +205,12 @@ bool ContextBase::isValidState()
if (!determineOutputType()) {
return false;
}
+ if (hasColumnOpsMethods()) {
+ FileRecordMgr *dbFile = getFile(hasIntersectMethods() ? _databaseFileIdx : 0);
+ if (!_keyListOps->isValidColumnOps(dbFile)) {
+ return false;
+ }
+ }
return true;
}
@@ -354,3 +383,85 @@ bool ContextBase::handle_ubam()
markUsed(_i - _skipFirstArgs);
return true;
}
+
+
+// Methods specific to column operations.
+// for col ops, -c is the string of columns upon which to operate
+bool ContextBase::handle_c()
+{
+ if (!hasColumnOpsMethods()) {
+ return false;
+ }
+ if ((_i+1) < _argc) {
+ _keyListOps->setColumns(_argv[_i + 1]);
+ markUsed(_i - _skipFirstArgs);
+ _i++;
+ markUsed(_i - _skipFirstArgs);
+ }
+ return true;
+}
+
+
+// for col ops, -o is the string of operations to apply to the columns (-c)
+bool ContextBase::handle_o()
+{
+ if (!hasColumnOpsMethods()) {
+ return false;
+ }
+ if ((_i+1) < _argc) {
+ _keyListOps->setOperations(_argv[_i + 1]);
+ markUsed(_i - _skipFirstArgs);
+ _i++;
+ markUsed(_i - _skipFirstArgs);
+ }
+ return true;
+}
+
+
+// for col ops, -null is a NULL vakue assigned
+// when no overlaps are detected.
+bool ContextBase::handle_null()
+{
+ if (!hasColumnOpsMethods()) {
+ return false;
+ }
+ if ((_i+1) < _argc) {
+ _keyListOps->setNullValue(_argv[_i + 1]);
+ markUsed(_i - _skipFirstArgs);
+ _i++;
+ markUsed(_i - _skipFirstArgs);
+ }
+ return true;
+}
+
+//for col ops, delimStr will appear between each item in
+//a collapsed but delimited list.
+bool ContextBase::handle_delim()
+{
+ if (!hasColumnOpsMethods()) {
+ return false;
+ }
+ if ((_i+1) < _argc) {
+ _keyListOps->setDelimStr(_argv[_i + 1]);
+ markUsed(_i - _skipFirstArgs);
+ _i++;
+ markUsed(_i - _skipFirstArgs);
+ }
+ return true;
+}
+
+void ContextBase::setColumnOpsMethods(bool val)
+{
+ _hasColumnOpsMethods = val;
+ if (val) {
+ _keyListOps = new KeyListOps();
+ }
+}
+
+const QuickString &ContextBase::getColumnOpsVal(RecordKeyList &keyList) const {
+ if (!hasColumnOpsMethods()) {
+ return _nullStr;
+ }
+ return _keyListOps->getOpVals(keyList);
+}
+
diff --git a/src/utils/Contexts/ContextBase.h b/src/utils/Contexts/ContextBase.h
index 7846f6218f02e184248ceeb228f6dddb5206e48a..b4bf12279f71db6a934a4e42a8970771a4a528e8 100644
--- a/src/utils/Contexts/ContextBase.h
+++ b/src/utils/Contexts/ContextBase.h
@@ -24,6 +24,7 @@
#include "NewGenomeFile.h"
#include "api/BamReader.h"
#include "api/BamAux.h"
+#include "KeyListOps.h"
class ContextBase {
@@ -144,6 +145,13 @@ public:
//methods.
virtual bool hasIntersectMethods() const { return false; }
+ // determine whether column operations like those used in map
+ // are available.
+ void setColumnOpsMethods(bool val);
+ virtual bool hasColumnOpsMethods() const { return _hasColumnOpsMethods; }
+ const QuickString &getColumnOpsVal(RecordKeyList &keyList) const;
+ //methods applicable only to column operations.
+
protected:
PROGRAM_TYPE _program;
@@ -204,6 +212,10 @@ protected:
bool _forwardOnly;
bool _reverseOnly;
+ bool _hasColumnOpsMethods;
+ KeyListOps *_keyListOps;
+ QuickString _nullStr; //placeholder return value when col ops aren't valid.
+
void markUsed(int i) { _argsProcessed[i] = true; }
bool isUsed(int i) const { return _argsProcessed[i]; }
bool cmdArgsValid();
@@ -227,6 +239,11 @@ protected:
virtual bool handle_split();
virtual bool handle_sorted();
virtual bool handle_ubam();
+
+ virtual bool handle_c();
+ virtual bool handle_o();
+ virtual bool handle_null();
+ virtual bool handle_delim();
};
#endif /* CONTEXTBASE_H_ */
diff --git a/src/utils/Contexts/ContextMap.cpp b/src/utils/Contexts/ContextMap.cpp
index 8b2027241934986a3abfe083cfa41b37e35c2b79..e3f82417cda79b1ab81e89d72847613b6c151c53 100644
--- a/src/utils/Contexts/ContextMap.cpp
+++ b/src/utils/Contexts/ContextMap.cpp
@@ -8,18 +8,11 @@
#include "ContextMap.h"
ContextMap::ContextMap()
-: _delimStr(",")
{
// map requires sorted input
setSortedInput(true);
setLeftJoin(true);
-
- // default to BED score column
- setColumns("5");
- // default to "sum"
- setOperations("sum");
- // default to "." as a NULL value
- setNullValue('.');
+ setColumnOpsMethods(true);
}
ContextMap::~ContextMap()
@@ -45,131 +38,22 @@ bool ContextMap::parseCmdArgs(int argc, char **argv, int skipFirstArgs) {
if (isUsed(_i - _skipFirstArgs)) {
continue;
}
- else if (strcmp(_argv[_i], "-o") == 0) {
- if (!handle_o()) return false;
- }
- else if (strcmp(_argv[_i], "-c") == 0) {
- if (!handle_c()) return false;
- }
- else if (strcmp(_argv[_i], "-null") == 0) {
- if (!handle_null()) return false;
- }
- else if (strcmp(_argv[_i], "-delim") == 0) {
- if (!handle_delim()) return false;
- }
+ if (strcmp(_argv[_i], "-c") == 0) {
+ //bypass intersect's use of the -c option, because -c
+ //means writeCount for intersect, but means columns for map.
+ if (!ContextBase::handle_c()) return false;
+ }
}
return ContextIntersect::parseCmdArgs(argc, argv, _skipFirstArgs);
}
-
-
-bool ContextMap::isValidState()
-{
- if (!ContextIntersect::isValidState()) {
- return false;
- }
-
- if (getDatabaseFileType() == FileRecordTypeChecker::BAM_FILE_TYPE) {
- //throw Error
- cerr << endl << "*****" << endl
- << "***** ERROR: BAM database file not currently supported for the map tool."
- << endl;
- exit(1);
- }
-
-
- //get the strings from context containing the comma-delimited lists of columns
- //and operations. Split both of these into vectors. Get the operation code
- //for each operation string. Finally, make a vector of pairs, where the first
- //member of each pair is a column number, and the second member is the code for the
- //operation to perform on that column.
-
- vector<QuickString> columnsVec;
- vector<QuickString> opsVec;
- int numCols = Tokenize(_columns, columnsVec, ',');
- int numOps = Tokenize(_operations, opsVec, ',');
-
- if (numOps < 1 || numCols < 1) {
- cerr << endl << "*****" << endl
- << "***** ERROR: There must be at least one column and at least one operation named." << endl;
- return false;
- }
- if (numOps > 1 && numCols != numOps) {
- cerr << endl << "*****" << endl
- << "***** ERROR: There are " << numCols <<" columns given, but there are " << numOps << " operations. " << endl;
- cerr << "\tPlease provide either a single operation that will be applied to all listed columns, " << endl;
- cerr << "\tor an operation for each column." << endl;
- return false;
- }
- KeyListOps keyListOps;
- for (int i=0; i < (int)columnsVec.size(); i++) {
- int col = str2chrPos(columnsVec[i]);
-
- //check that the column number is valid
- if (col < 1 || col > getDatabaseFile()->getNumFields()) {
- cerr << endl << "*****" << endl << "***** ERROR: Requested column " << col << ", but database file "
- << getDatabaseFileName() << " only has fields 1 - " << getDatabaseFile()->getNumFields() << "." << endl;
- return false;
- }
- const QuickString &operation = opsVec.size() > 1 ? opsVec[i] : opsVec[0];
- KeyListOps::OP_TYPES opCode = keyListOps.getOpCode(operation);
- if (opCode == KeyListOps::INVALID) {
- cerr << endl << "*****" << endl
- << "***** ERROR: " << operation << " is not a valid operation. " << endl;
- return false;
- }
- _colOps.push_back(pair<int, KeyListOps::OP_TYPES>(col, opCode));
- }
- return true;
-}
-
-
-// for map, -c is the string of columns upon which to operate
-bool ContextMap::handle_c()
-{
- if ((_i+1) < _argc) {
- setColumns(_argv[_i + 1]);
- markUsed(_i - _skipFirstArgs);
- _i++;
- markUsed(_i - _skipFirstArgs);
- }
- return true;
-}
-
-
-// for map, -o is the string of operations to apply to the columns (-c)
-bool ContextMap::handle_o()
-{
- if ((_i+1) < _argc) {
- setOperations(_argv[_i + 1]);
- markUsed(_i - _skipFirstArgs);
- _i++;
- markUsed(_i - _skipFirstArgs);
- }
- return true;
-}
-
-
-// for map, -null is a NULL vakue assigned
-// when no overlaps are detected.
-bool ContextMap::handle_null()
-{
- if ((_i+1) < _argc) {
- setNullValue(_argv[_i + 1]);
- markUsed(_i - _skipFirstArgs);
- _i++;
- markUsed(_i - _skipFirstArgs);
- }
- return true;
-}
-
-bool ContextMap::handle_delim()
-{
- if ((_i+1) < _argc) {
- _delimStr = _argv[_i + 1];
- markUsed(_i - _skipFirstArgs);
- _i++;
- markUsed(_i - _skipFirstArgs);
- }
- return true;
-}
+//
+//
+//bool ContextMap::isValidState()
+//{
+// if (!ContextIntersect::isValidState()) {
+// return false;
+// }
+//}
+//
+//
diff --git a/src/utils/Contexts/ContextMap.h b/src/utils/Contexts/ContextMap.h
index 460f93b29100cf4ad2d6fbc2bd5e9e1805956938..9b7280e5425991a3f47588c7c3c78cf9b9fd8745 100644
--- a/src/utils/Contexts/ContextMap.h
+++ b/src/utils/Contexts/ContextMap.h
@@ -15,37 +15,14 @@ class ContextMap : public ContextIntersect {
public:
ContextMap();
virtual ~ContextMap();
- virtual bool isValidState();
-
+// virtual bool isValidState();
+//
virtual bool parseCmdArgs(int argc, char **argv, int skipFirstArgs);
-
- const QuickString &getColumns() const { return _columns; }
- void setColumns(const QuickString &columns) { _columns = columns; }
-
- const QuickString & getOperations() const { return _operations; }
- void setOperations(const QuickString & operation) { _operations = operation; }
-
- const QuickString & getNullValue() const { return _nullValue; }
- void setNullValue(const QuickString & nullValue) { _nullValue = nullValue; }
-
- const QuickString &getDelim() const { return _delimStr; }
+//
virtual bool hasIntersectMethods() const { return true; }
-
- typedef vector<pair<int, KeyListOps::OP_TYPES> > colOpsType;
- const colOpsType &getColOps() const { return _colOps; }
+//
private:
- QuickString _operations;
- QuickString _columns;
- QuickString _nullValue;
- KeyListOps _keyListOps;
- colOpsType _colOps;
- QuickString _delimStr;
-
- virtual bool handle_c();
- virtual bool handle_o();
- virtual bool handle_null();
- virtual bool handle_delim();
};
diff --git a/src/utils/FileRecordTools/Records/BamRecord.cpp b/src/utils/FileRecordTools/Records/BamRecord.cpp
index 4c5cd8dc2fb4b3716ed1fc3de598428be747eb4e..f939fefbe6d117e88f224f8e5b14c2562f4be4c7 100644
--- a/src/utils/FileRecordTools/Records/BamRecord.cpp
+++ b/src/utils/FileRecordTools/Records/BamRecord.cpp
@@ -172,5 +172,10 @@ const QuickString &BamRecord::getField(int fieldNum) const
return Bed6Interval::getField(fieldNum);
}
+bool BamRecord::isNumericField(int fieldNum) {
+
+ //TBD: As with getField, this isn't defined for BAM.
+ return (fieldNum > 6 ? false : Bed6Interval::isNumericField(fieldNum));
+}
diff --git a/src/utils/FileRecordTools/Records/BamRecord.h b/src/utils/FileRecordTools/Records/BamRecord.h
index b74dbc2c92b05e83ba64e7eca1e1ddf6e59dd525..022ecb4d94da5f96133c487e774de7ff4377be00 100644
--- a/src/utils/FileRecordTools/Records/BamRecord.h
+++ b/src/utils/FileRecordTools/Records/BamRecord.h
@@ -40,6 +40,7 @@ public:
virtual const QuickString &getField(int fieldNum) const;
virtual int getNumFields() const { return 12; }
+ static bool isNumericField(int fieldNum);
protected:
BamTools::BamAlignment _bamAlignment;
diff --git a/src/utils/FileRecordTools/Records/Bed12Interval.cpp b/src/utils/FileRecordTools/Records/Bed12Interval.cpp
index 867a69ec4c23e50d2f1c3588f9622a78ce992176..0a5a092feef3ba1d02d599f7d50243c949aeb4f6 100644
--- a/src/utils/FileRecordTools/Records/Bed12Interval.cpp
+++ b/src/utils/FileRecordTools/Records/Bed12Interval.cpp
@@ -146,3 +146,29 @@ const QuickString &Bed12Interval::getField(int fieldNum) const
}
}
+bool Bed12Interval::isNumericField(int fieldNum) {
+ switch (fieldNum) {
+ case 7:
+ return true;
+ break;
+ case 8:
+ return true;
+ break;
+ case 9:
+ return false;
+ break;
+ case 10:
+ return true;
+ break;
+ case 11:
+ return false;
+ break;
+ case 12:
+ return false;
+ break;
+ default:
+ return Bed6Interval::isNumericField(fieldNum);
+ break;
+ }
+}
+
diff --git a/src/utils/FileRecordTools/Records/Bed12Interval.h b/src/utils/FileRecordTools/Records/Bed12Interval.h
index 711800c3d7560d0834f5b823d48ffa47f3ec3535..ffa89f9044a0d8df0d25a3f4fadb90e2b27afaa0 100644
--- a/src/utils/FileRecordTools/Records/Bed12Interval.h
+++ b/src/utils/FileRecordTools/Records/Bed12Interval.h
@@ -54,6 +54,7 @@ public:
virtual const QuickString &getField(int fieldNum) const;
virtual int getNumFields() const { return 12; }
+ static bool isNumericField(int fieldNum);
protected:
diff --git a/src/utils/FileRecordTools/Records/Bed3Interval.cpp b/src/utils/FileRecordTools/Records/Bed3Interval.cpp
index 3f896be5a80614cccc8b058eb04b746f2ec19b84..e31e43eafa5e5bb2a1b7eeadc9940a5332fe17b5 100644
--- a/src/utils/FileRecordTools/Records/Bed3Interval.cpp
+++ b/src/utils/FileRecordTools/Records/Bed3Interval.cpp
@@ -79,3 +79,23 @@ const QuickString &Bed3Interval::getField(int fieldNum) const
break;
}
}
+
+bool Bed3Interval::isNumericField(int fieldNum) {
+ switch (fieldNum) {
+ case 1:
+ return false; //chrom
+ break;
+ case 2:
+ return true; //startPos
+ break;
+ case 3:
+ return true; //endPos
+ break;
+ default:
+ cerr << endl << "*****" << endl
+ << "*****ERROR: requested invalid column " << fieldNum << ". Exiting." << endl
+ << endl << "*****" << endl;
+ exit(1);
+ break;
+ }
+}
diff --git a/src/utils/FileRecordTools/Records/Bed3Interval.h b/src/utils/FileRecordTools/Records/Bed3Interval.h
index 9f1ff1183a975fa7defda698abee05831bd5b771..93377a0a171df9cc8bffae94b51f53d667b313c7 100644
--- a/src/utils/FileRecordTools/Records/Bed3Interval.h
+++ b/src/utils/FileRecordTools/Records/Bed3Interval.h
@@ -32,6 +32,8 @@ public:
virtual const QuickString &getField(int fieldNum) const;
virtual int getNumFields() const { return 3; }
+ static bool isNumericField(int fieldNum);
+
protected:
virtual ~Bed3Interval();
diff --git a/src/utils/FileRecordTools/Records/Bed4Interval.cpp b/src/utils/FileRecordTools/Records/Bed4Interval.cpp
index c1ef81a3c51d91fd563c351d7ae751e80892cfe6..27ca9f7f845a81c9686368db9f68a873ade7551d 100644
--- a/src/utils/FileRecordTools/Records/Bed4Interval.cpp
+++ b/src/utils/FileRecordTools/Records/Bed4Interval.cpp
@@ -60,3 +60,8 @@ const QuickString &Bed4Interval::getField(int fieldNum) const
}
}
+bool Bed4Interval::isNumericField(int fieldNum) {
+ return (fieldNum == 4 ? false : Bed3Interval::isNumericField(fieldNum));
+}
+
+
diff --git a/src/utils/FileRecordTools/Records/Bed4Interval.h b/src/utils/FileRecordTools/Records/Bed4Interval.h
index f42817c495ed4780dd57aa82d3c4a93718840e5b..b03844645165650742db79a6337814a826ecd05d 100644
--- a/src/utils/FileRecordTools/Records/Bed4Interval.h
+++ b/src/utils/FileRecordTools/Records/Bed4Interval.h
@@ -28,6 +28,7 @@ public:
virtual const QuickString &getField(int fieldNum) const;
virtual int getNumFields() const { return 4; }
+ static bool isNumericField(int fieldNum);
protected:
diff --git a/src/utils/FileRecordTools/Records/Bed5Interval.cpp b/src/utils/FileRecordTools/Records/Bed5Interval.cpp
index 7307fb667ee5bbbf40fe0576fd9654bec0c9ad0f..130a788d945c523a5bdbb011c349c28cbe1f5edb 100644
--- a/src/utils/FileRecordTools/Records/Bed5Interval.cpp
+++ b/src/utils/FileRecordTools/Records/Bed5Interval.cpp
@@ -70,3 +70,16 @@ const QuickString &Bed5Interval::getField(int fieldNum) const
break;
}
}
+
+bool Bed5Interval::isNumericField(int fieldNum) {
+ switch (fieldNum) {
+ case 4:
+ return false;
+ break;
+ case 5:
+ return true;
+ break;
+ default:
+ return Bed3Interval::isNumericField(fieldNum);
+ }
+}
diff --git a/src/utils/FileRecordTools/Records/Bed5Interval.h b/src/utils/FileRecordTools/Records/Bed5Interval.h
index bc913d1df6f4b22c355d0ace56d5e0143feced12..2064d3546da9674bda43adfb844e212ce5d32876 100644
--- a/src/utils/FileRecordTools/Records/Bed5Interval.h
+++ b/src/utils/FileRecordTools/Records/Bed5Interval.h
@@ -27,6 +27,7 @@ public:
virtual const QuickString &getField(int fieldNum) const;
virtual int getNumFields() const { return 5; }
+ static bool isNumericField(int fieldNum);
protected:
diff --git a/src/utils/FileRecordTools/Records/Bed6Interval.cpp b/src/utils/FileRecordTools/Records/Bed6Interval.cpp
index 8371553a435941c0b713d64a55d198e4760a75ac..5bc783c748e09fc0d52fe54d3a52b628e06b9744 100644
--- a/src/utils/FileRecordTools/Records/Bed6Interval.cpp
+++ b/src/utils/FileRecordTools/Records/Bed6Interval.cpp
@@ -81,3 +81,20 @@ const QuickString &Bed6Interval::getField(int fieldNum) const
break;
}
}
+
+bool Bed6Interval::isNumericField(int fieldNum) {
+ switch (fieldNum) {
+ case 4:
+ return false;
+ break;
+ case 5:
+ return true;
+ break;
+ case 6:
+ return false;
+ break;
+ default:
+ return Bed3Interval::isNumericField(fieldNum);
+ break;
+ }
+}
diff --git a/src/utils/FileRecordTools/Records/Bed6Interval.h b/src/utils/FileRecordTools/Records/Bed6Interval.h
index 9ad9f80b523ae5f5aef43aa3fd61e29cdc09e27f..023683fe6b48191bddcb9cd68dd5d102cd79df2f 100644
--- a/src/utils/FileRecordTools/Records/Bed6Interval.h
+++ b/src/utils/FileRecordTools/Records/Bed6Interval.h
@@ -27,6 +27,7 @@ public:
virtual const QuickString &getField(int fieldNum) const;
virtual int getNumFields() const { return 6; }
+ static bool isNumericField(int fieldNum);
protected:
diff --git a/src/utils/FileRecordTools/Records/BedGraphInterval.cpp b/src/utils/FileRecordTools/Records/BedGraphInterval.cpp
index e0808573c0a6cb35de787421a4a60e260d08ffa7..9cfda4803d4e5d3e876ea5bc26227d7ede8a1faa 100644
--- a/src/utils/FileRecordTools/Records/BedGraphInterval.cpp
+++ b/src/utils/FileRecordTools/Records/BedGraphInterval.cpp
@@ -60,3 +60,14 @@ const QuickString &BedGraphInterval::getField(int fieldNum) const
}
}
+bool BedGraphInterval::isNumericField(int fieldNum) {
+ switch (fieldNum) {
+ case 4:
+ return true;
+ break;
+ default:
+ return Bed3Interval::isNumericField(fieldNum);
+ break;
+ }
+}
+
diff --git a/src/utils/FileRecordTools/Records/BedGraphInterval.h b/src/utils/FileRecordTools/Records/BedGraphInterval.h
index 1bdf619a807885347ace0a55fbcaf302c4ff95a2..5db6feafa09666b8a981b4dc755ed8998b24d113 100644
--- a/src/utils/FileRecordTools/Records/BedGraphInterval.h
+++ b/src/utils/FileRecordTools/Records/BedGraphInterval.h
@@ -28,6 +28,7 @@ public:
virtual const QuickString &getField(int fieldNum) const;
virtual int getNumFields() const { return 4; }
+ static bool isNumericField(int fieldNum);
protected:
virtual ~BedGraphInterval();
diff --git a/src/utils/FileRecordTools/Records/BedPlusInterval.cpp b/src/utils/FileRecordTools/Records/BedPlusInterval.cpp
index fc8be368e09d12ed8ae31446c83313296fb8d2a5..5819b863c1da839ab31d6fb29f61752a6d73eb02 100644
--- a/src/utils/FileRecordTools/Records/BedPlusInterval.cpp
+++ b/src/utils/FileRecordTools/Records/BedPlusInterval.cpp
@@ -117,3 +117,18 @@ const QuickString &BedPlusInterval::getField(int fieldNum) const
}
return Bed6Interval::getField(fieldNum);
}
+
+bool BedPlusInterval::isNumericField(int fieldNum) {
+
+ //
+ // TBD: There is no currently no good way to guarantee / enforce whether
+ // fields after the 6th are numeric, so for now we'll give the user the
+ // benefit of the doubt on those.
+ //
+ if (fieldNum > startOtherIdx) {
+ return true;
+ } else {
+ return Bed6Interval::isNumericField(fieldNum);
+ }
+}
+
diff --git a/src/utils/FileRecordTools/Records/BedPlusInterval.h b/src/utils/FileRecordTools/Records/BedPlusInterval.h
index 4b98b4f3d0a745ea80709f68bfd0bfa7a7e23d09..077ed9367ac5b99a707d04f0387fb7ea0a09ccb7 100644
--- a/src/utils/FileRecordTools/Records/BedPlusInterval.h
+++ b/src/utils/FileRecordTools/Records/BedPlusInterval.h
@@ -38,6 +38,8 @@ public:
virtual void setField(int fieldNum, const char *str) { (*(_otherIdxs[fieldNum])) = str; }
virtual void setNumPrintFields(int num) { _numPrintFields = num; }
virtual int getNumPrintFields() const { return _numPrintFields; }
+ static bool isNumericField(int fieldNum);
+
protected:
virtual ~BedPlusInterval();
diff --git a/src/utils/FileRecordTools/Records/GffRecord.cpp b/src/utils/FileRecordTools/Records/GffRecord.cpp
index a91ce159eb819309959d0391f70d69e8217b6808..21cea1dab87ea07e05e5b6331ecca4f9abe56cb5 100644
--- a/src/utils/FileRecordTools/Records/GffRecord.cpp
+++ b/src/utils/FileRecordTools/Records/GffRecord.cpp
@@ -156,4 +156,40 @@ const QuickString &GffRecord::getField(int fieldNum) const
}
}
+bool GffRecord::isNumericField(int fieldNum) {
+ switch (fieldNum) {
+ case 1:
+ return false;
+ break;
+ case 2:
+ return false;
+ break;
+ case 3:
+ return false;
+ break;
+ case 4:
+ return true;
+ break;
+ case 5:
+ return true;
+ break;
+ case 6:
+ return true;
+ break;
+ case 7:
+ return false;
+ break;
+ case 8:
+ return false;
+ break;
+ case 9:
+ return false;
+ break;
+ default:
+ return Bed6Interval::isNumericField(fieldNum);
+ break;
+ }
+
+}
+
diff --git a/src/utils/FileRecordTools/Records/GffRecord.h b/src/utils/FileRecordTools/Records/GffRecord.h
index b84d96a71384750e850de0ffe4d03bb3e8272dfd..e675542f37e6939897e0e5adb1f537ef642761d4 100644
--- a/src/utils/FileRecordTools/Records/GffRecord.h
+++ b/src/utils/FileRecordTools/Records/GffRecord.h
@@ -34,6 +34,7 @@ public:
//Note: using the assignment operator in a GffRecord can potentially be a performance hit,
//if the number of fields frequently differ between this object and the one being copied.
const GffRecord &operator=(const GffRecord &other);
+ static bool isNumericField(int fieldNum);
protected:
virtual ~GffRecord();
diff --git a/src/utils/FileRecordTools/Records/Record.cpp b/src/utils/FileRecordTools/Records/Record.cpp
index 2beb4dca13cad05913be21e5870c66657a2dfdc7..89544ed21f23e91d7db73ab1e6e2158edc695ae9 100644
--- a/src/utils/FileRecordTools/Records/Record.cpp
+++ b/src/utils/FileRecordTools/Records/Record.cpp
@@ -187,9 +187,9 @@ void Record::undoZeroLength()
ostream &operator << (ostream &out, const Record &record)
{
- QuickString errBuf;
- record.print(errBuf);
- out << errBuf;
+ QuickString outBuf;
+ record.print(outBuf);
+ out << outBuf;
return out;
}
diff --git a/src/utils/FileRecordTools/Records/Record.h b/src/utils/FileRecordTools/Records/Record.h
index 2c303d90c02272ea1c7a3956d29e8fac1abd0398..d8071c1ed223d7172bd7faa33e6ff6f514975616 100644
--- a/src/utils/FileRecordTools/Records/Record.h
+++ b/src/utils/FileRecordTools/Records/Record.h
@@ -129,6 +129,8 @@ public:
virtual bool sameChromIntersects(const Record *otherRecord,
bool sameStrand, bool diffStrand, float overlapFraction, bool reciprocal) const;
+// virtual static bool isNumericField(int fieldNum) const = 0;
+
protected:
virtual ~Record(); //by making the destructor protected, only the friend class(es) can actually delete Record objects, or objects derived from Record.
diff --git a/src/utils/GenomeFile/Makefile b/src/utils/GenomeFile/Makefile
index afaeccd4af5e138a17fa8cd0fd437141840935d2..fd17d29941e5dc51eadd02f66f6a142fd9160266 100644
--- a/src/utils/GenomeFile/Makefile
+++ b/src/utils/GenomeFile/Makefile
@@ -6,6 +6,7 @@ UTILITIES_DIR = ../
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/general/ \
-I$(UTILITIES_DIR)/lineFileUtilities/ \
+ -I$(UTILITIES_DIR)/KeyListOps/ \
-I$(UTILITIES_DIR)/BamTools/include/
# ----------------------------------
diff --git a/src/utils/KeyListOps/KeyListOps.cpp b/src/utils/KeyListOps/KeyListOps.cpp
index 05a60402e867a641c616bb2b7d86cf599089d759..657635000e5313c200567d25ea36a29623bd4056 100644
--- a/src/utils/KeyListOps/KeyListOps.cpp
+++ b/src/utils/KeyListOps/KeyListOps.cpp
@@ -1,37 +1,14 @@
/*
* KeyListOps.cpp
*
- * Created on: Feb 6, 2014
+ * Created on: Feb 24, 2014
* Author: nek3d
*/
-
#include "KeyListOps.h"
-#include <cfloat>
-#include <cmath>
-#include <algorithm>
-
-KeyListOps::KeyListOps()
-: _keyList(&_nullKeyList),
- _column(1),
- _nullVal("."),
- _delimStr(","),
- _iter(_nullKeyList.begin())
-{
- init();
+#include "FileRecordMgr.h"
+#include <cmath> //for isnan
-}
-
-KeyListOps::KeyListOps(RecordKeyList *keyList, int column)
-: _keyList(keyList),
- _column(column),
- _nullVal("."),
- _delimStr(","),
- _iter(keyList->begin())
-{
- init();
-}
-
-void KeyListOps::init() {
+KeyListOps::KeyListOps() {
_opCodes["sum"] = SUM;
_opCodes["mean"] = MEAN;
_opCodes["stddev"] = STDDEV;
@@ -53,11 +30,44 @@ void KeyListOps::init() {
_opCodes["freq_desc"] = FREQ_DESC;
_opCodes["first"] = FIRST;
_opCodes["last"] = LAST;
-}
+ _isNumericOp[SUM] = true;
+ _isNumericOp[MEAN] = true;
+ _isNumericOp[STDDEV] = true;
+ _isNumericOp[MEDIAN] = true;
+ _isNumericOp[MODE] = false;
+ _isNumericOp[ANTIMODE] = false;
+ _isNumericOp[MIN] = true;
+ _isNumericOp[MAX] = true;
+ _isNumericOp[ABSMIN] = true;
+ _isNumericOp[COUNT] = false;
+ _isNumericOp[DISTINCT] = false;
+ _isNumericOp[COUNT_DISTINCT] = false;
+ _isNumericOp[DISTINCT_ONLY] = false;
+ _isNumericOp[COLLAPSE] = false;
+ _isNumericOp[CONCAT] = false;
+ _isNumericOp[FREQ_ASC] = false;
+ _isNumericOp[FREQ_DESC] = false;
+ _isNumericOp[FIRST] = false;
+ _isNumericOp[LAST] = false;
+
+ _methods.setDelimStr(",");
+ _methods.setNullValue(".");
+
+ // default to BED score column
+ _columns = "5";
+ // default to "sum"
+ _operations = "sum";
+
+}
-KeyListOps::~KeyListOps() {
+bool KeyListOps::isNumericOp(OP_TYPES op) const {
+ map<OP_TYPES, bool>::const_iterator iter = _isNumericOp.find(op);
+ return (iter == _isNumericOp.end() ? false : iter->second);
+}
+bool KeyListOps::isNumericOp(const QuickString &op) const {
+ return isNumericOp(getOpCode(op));
}
KeyListOps::OP_TYPES KeyListOps::getOpCode(const QuickString &operation) const {
@@ -70,336 +80,285 @@ KeyListOps::OP_TYPES KeyListOps::getOpCode(const QuickString &operation) const {
return iter->second;
}
-// return the total of the values in the vector
-double KeyListOps::getSum() {
- if (empty()) return NAN;
- double theSum = 0.0;
- for (begin(); !end(); next()) {
- theSum += getColValNum();
- }
- return theSum;
-}
+bool KeyListOps::isValidColumnOps(FileRecordMgr *dbFile) {
-// return the average value in the vector
-double KeyListOps::getMean() {
- if (empty()) return NAN;
+ if (dbFile->getFileType() == FileRecordTypeChecker::BAM_FILE_TYPE) {
+ //throw Error
+ cerr << endl << "*****" << endl
+ << "***** ERROR: BAM database file not currently supported for column operations."
+ << endl;
+ exit(1);
+ }
- return getSum() / (float)getCount();
-}
+ //get the strings from context containing the comma-delimited lists of columns
+ //and operations. Split both of these into vectors. Get the operation code
+ //for each operation string. Finally, make a vector of pairs, where the first
+ //member of each pair is a column number, and the second member is the code for the
+ //operation to perform on that column.
- // return the standard deviation
-double KeyListOps::getStddev() {
- if (empty()) return NAN;
+ vector<QuickString> columnsVec;
+ vector<QuickString> opsVec;
+ int numCols = Tokenize(_columns, columnsVec, ',');
+ int numOps = Tokenize(_operations, opsVec, ',');
- double avg = getMean();
- double squareDiffSum = 0.0;
- for (begin(); !end(); next()) {
- double val = getColValNum();
- double diff = val - avg;
- squareDiffSum += diff * diff;
+ if (numOps < 1 || numCols < 1) {
+ cerr << endl << "*****" << endl
+ << "***** ERROR: There must be at least one column and at least one operation named." << endl;
+ return false;
}
- return squareDiffSum / (float)getCount();
-}
-// return the standard deviation
-double KeyListOps::getSampleStddev() {
- if (empty()) return NAN;
-
- double avg = getMean();
- double squareDiffSum = 0.0;
- for (begin(); !end(); next()) {
- double val = getColValNum();
- double diff = val - avg;
- squareDiffSum += diff * diff;
- }
- return squareDiffSum / ((float)getCount() - 1.0);
-}
-
-// return the median value in the vector
-double KeyListOps::getMedian() {
- if (empty()) return NAN;
-
- //get sorted vector. if even number of elems, return middle val.
- //if odd, average of two.
- toArray(true, ASC);
- size_t count = getCount();
- if (count % 2) {
- //odd number of elements. Take middle one.
- return _numArray[count/2];
- } else {
- //even numnber of elements. Take average of middle 2.
- double sum = _numArray[count/2 -1] + _numArray[count/2];
- return sum / 2.0;
+ if (numOps > 1 && numCols != numOps) {
+ cerr << endl << "*****" << endl
+ << "***** ERROR: There are " << numCols <<" columns given, but there are " << numOps << " operations." << endl;
+ cerr << "\tPlease provide either a single operation that will be applied to all listed columns, " << endl;
+ cerr << "\tor an operation for each column." << endl;
+ return false;
}
-}
-
-// return the most common value in the vector
-const QuickString &KeyListOps::getMode() {
- if (empty()) return _nullVal;
-
- makeFreqMap();
-
- //now pass through the freq map and keep track of which key has the highest occurance.
- freqMapType::iterator maxIter = _freqMap.begin();
- int maxVal = 0;
- for (; _freqIter != _freqMap.end(); _freqIter++) {
- if (_freqIter->second > maxVal) {
- maxIter = _freqIter;
- maxVal = _freqIter->second;
+ for (int i=0; i < (int)columnsVec.size(); i++) {
+ int col = str2chrPos(columnsVec[i]);
+
+ //check that the column number is valid
+ if (col < 1 || col > dbFile->getNumFields()) {
+ cerr << endl << "*****" << endl << "***** ERROR: Requested column " << col << ", but database file "
+ << dbFile->getFileName() << " only has fields 1 - " << dbFile->getNumFields() << "." << endl;
+ return false;
}
- }
- _retStr = maxIter->first;
- return _retStr;
-}
-// return the least common value in the vector
-const QuickString &KeyListOps::getAntiMode() {
- if (empty()) return _nullVal;
-
- makeFreqMap();
-
- //now pass through the freq map and keep track of which key has the highest occurance.
- freqMapType::iterator minIter = _freqMap.begin();
- int minVal = INT_MAX;
- for (; _freqIter != _freqMap.end(); _freqIter++) {
- if (_freqIter->second < minVal) {
- minIter = _freqIter;
- minVal = _freqIter->second;
+ const QuickString &operation = opsVec.size() > 1 ? opsVec[i] : opsVec[0];
+ OP_TYPES opCode = getOpCode(operation);
+ if (opCode == INVALID) {
+ cerr << endl << "*****" << endl
+ << "***** ERROR: " << operation << " is not a valid operation. " << endl;
+ return false;
}
+ _colOps.push_back(pair<int, OP_TYPES>(col, opCode));
}
- _retStr = minIter->first;
- return _retStr;
-}
-// return the minimum element of the vector
-double KeyListOps::getMin() {
- if (empty()) return NAN;
-
- double minVal = DBL_MAX;
- for (begin(); !end(); next()) {
- double currVal = getColValNum();
- minVal = (currVal < minVal) ? currVal : minVal;
- }
- return minVal;
-}
-
-// return the maximum element of the vector
-double KeyListOps::getMax() {
- if (empty()) return NAN;
-
- double maxVal = DBL_MIN;
- for (begin(); !end(); next()) {
- double currVal = getColValNum();
- maxVal = (currVal > maxVal) ? currVal : maxVal;
- }
- return maxVal;
-}
-
-// return the minimum absolute value of the vector
-double KeyListOps::getAbsMin() {
- if (empty()) return NAN;
-
- double minVal = DBL_MAX;
- for (begin(); !end(); next()) {
- double currVal = abs(getColValNum());
- minVal = (currVal < minVal) ? currVal : minVal;
- }
- return minVal;
-}
-// return the maximum absolute value of the vector
-double KeyListOps::getAbsMax() {
- if (empty()) return NAN;
-
- double maxVal = DBL_MIN;
- for (begin(); !end(); next()) {
- double currVal = abs(getColValNum());
- maxVal = (currVal > maxVal) ? currVal : maxVal;
- }
- return maxVal;
-}
-// return the count of element in the vector
-uint32_t KeyListOps::getCount() {
- return _keyList->size();
-}
-// return a delimited list of the unique elements
-const QuickString &KeyListOps::getDistinct() {
- if (empty()) return _nullVal;
- // separated list of unique values. If something repeats, only report once.
- makeFreqMap();
- _retStr.clear();
- for (; _freqIter != _freqMap.end(); _freqIter++) {
- if (_freqIter != _freqMap.begin()) _retStr += _delimStr;
- _retStr.append(_freqIter->first);
- }
- return _retStr;
-}
-
-const QuickString &KeyListOps::getDistinctOnly() {
- if (empty()) return _nullVal;
-
- //separated list of only unique values. If item repeats, discard.
- makeFreqMap();
- _retStr.clear();
- for (; _freqIter != _freqMap.end(); _freqIter++) {
- if (_freqIter->second != 1) continue;
- if (_freqIter != _freqMap.begin()) _retStr += _delimStr;
- _retStr.append(_freqIter->first);
- }
- return _retStr;
-}
-
-// return a the count of _unique_ elements in the vector
-uint32_t KeyListOps::getCountDistinct() {
- if (empty()) return 0;
-
- makeFreqMap();
- return _freqMap.size();
-}
-// return a delimiter-separated list of elements
-const QuickString &KeyListOps::getCollapse(const QuickString &delimiter) {
- if (empty()) return _nullVal;
-
- //just put all items in one big separated list.
- _retStr.clear();
- int i=0;
- for (begin(); !end(); next()) {
- if (i > 0) _retStr += _delimStr;
- _retStr.append(getColVal());
- i++;
- }
- return _retStr;
-
-}
-// return a concatenation of all elements in the vector
-const QuickString &KeyListOps::getConcat() {
- if (empty()) return _nullVal;
-
- //like collapse but w/o commas. Just a true concat of all vals.
- //just swap out the delimChar with '' and call collapse, then
- //restore the delimChar.
- QuickString oldDelimStr(_delimStr);
- _delimStr = "";
- getCollapse(); //this will store it's results in the _retStr method.
- _delimStr = oldDelimStr;
- return _retStr;
-}
-
-// return a histogram of values and their freqs. in desc. order of frequency
-const QuickString &KeyListOps::getFreqDesc() {
- if (empty()) return _nullVal;
-
- //for each uniq val, report # occurances, in desc order.
- makeFreqMap();
- //put freq map into multimap where key is the freq and val is the item. In other words, basically a reverse freq map.
- histDescType hist;
- for (; _freqIter != _freqMap.end(); _freqIter++) {
- hist.insert(pair<int, QuickString>(_freqIter->second, _freqIter->first));
- }
- //now iterate through the reverse map we just made and output it's pairs in val:key format.
- _retStr.clear();
- for (histDescType::iterator histIter = hist.begin(); histIter != hist.end(); histIter++) {
- if (histIter != hist.begin()) _retStr += _delimStr;
- _retStr.append(histIter->second);
- _retStr += ":";
- _retStr.append(histIter->first);
- }
- return _retStr;
-}
-// return a histogram of values and their freqs. in asc. order of frequency
-const QuickString &KeyListOps::getFreqAsc() {
- if (empty()) return _nullVal;
-
- //for each uniq val, report # occurances, in asc order.
- makeFreqMap();
- //put freq map into multimap where key is the freq and val is the item. In other words, basically a reverse freq map.
- histAscType hist;
- for (; _freqIter != _freqMap.end(); _freqIter++) {
- hist.insert(pair<int, QuickString>(_freqIter->second, _freqIter->first));
-// hist[*(_freqIter->second)] = _freqIter->first;
- }
- //now iterate through the reverse map we just made and output it's pairs in val:key format.
- _retStr.clear();
- for (histAscType::iterator histIter = hist.begin(); histIter != hist.end(); histIter++) {
- if (histIter != hist.begin()) _retStr += _delimStr;
- _retStr.append(histIter->second);
- _retStr += ":";
- _retStr.append(histIter->first);
- }
- return _retStr;
-}
-// return the first value in the list
-const QuickString &KeyListOps::getFirst() {
- if (empty()) return _nullVal;
-
- //just the first item.
- begin();
- return getColVal();
-}
-// return the last value in the list
-const QuickString &KeyListOps::getLast() {
- if (empty()) return _nullVal;
-
- //just the last item.
- begin();
- for (size_t i = 0; i < getCount() -1; i++) {
- next();
- }
- return getColVal();
-}
-const QuickString &KeyListOps::getColVal() {
- return _iter->value()->getField(_column);
-}
-
-double KeyListOps::getColValNum() {
- return atof(_iter->value()->getField(_column).c_str());
-}
-void KeyListOps::toArray(bool useNum, SORT_TYPE sortVal) {
-
- //TBD: optimize performance with better memory management.
- if (useNum) {
- _numArray.resize(_keyList->size());
- int i=0;
- for (begin(); !end(); next()) {
- _numArray[i] = getColValNum();
- i++;
- }
- } else {
- _qsArray.resize(_keyList->size());
- int i=0;
- for (begin(); !end(); next()) {
- _qsArray[i] = getColVal();
- i++;
+ //The final step we need to do is check that for each column/operation pair,
+ //if the operation is numeric, see if the database's record type supports
+ //numeric operations for that column. For instance, we can allow the mean
+ //of column 4 for a BedGraph file, because that's numeric, but not for Bed4,
+ //because that isn't.
+
+ for (int i = 0; i < (int)_colOps.size(); i++) {
+ int col = _colOps[i].first;
+ OP_TYPES opCode = _colOps[i].second;
+ FileRecordTypeChecker::RECORD_TYPE recordType = dbFile->getRecordType();
+
+ if (isNumericOp(opCode)) {
+ bool isValidNumOp = false;
+ switch(recordType) {
+ case FileRecordTypeChecker::BED3_RECORD_TYPE:
+ isValidNumOp = Bed3Interval::isNumericField(col);
+ break;
+
+ case FileRecordTypeChecker::BED4_RECORD_TYPE:
+ isValidNumOp = Bed4Interval::isNumericField(col);
+ break;
+
+ case FileRecordTypeChecker::BED5_RECORD_TYPE:
+ isValidNumOp = Bed5Interval::isNumericField(col);
+ break;
+
+ case FileRecordTypeChecker::BEDGRAPH_RECORD_TYPE:
+ isValidNumOp = BedGraphInterval::isNumericField(col);
+ break;
+
+ case FileRecordTypeChecker::BED6_RECORD_TYPE:
+ isValidNumOp = Bed6Interval::isNumericField(col);
+ break;
+
+ case FileRecordTypeChecker::BED_PLUS_RECORD_TYPE:
+ isValidNumOp = BedPlusInterval::isNumericField(col);
+ break;
+
+ case FileRecordTypeChecker::BED12_RECORD_TYPE:
+ isValidNumOp = Bed12Interval::isNumericField(col);
+ break;
+
+ case FileRecordTypeChecker::BAM_RECORD_TYPE:
+ isValidNumOp = BamRecord::isNumericField(col);
+ break;
+
+ case FileRecordTypeChecker::VCF_RECORD_TYPE:
+ isValidNumOp = VcfRecord::isNumericField(col);
+ break;
+
+ case FileRecordTypeChecker::GFF_RECORD_TYPE:
+ isValidNumOp = GffRecord::isNumericField(col);
+ break;
+
+ default:
+ break;
+ }
+ if (!isValidNumOp) {
+ cerr << endl << "*****" << endl << "***** ERROR: Column " << col << " is not a numeric field for database file "
+ << dbFile->getFileName() << "." << endl;
+ return false;
+ }
}
}
- if (sortVal != UNSORTED) {
- sortArray(useNum, sortVal == ASC);
- }
+
+ return true;
}
-void KeyListOps::sortArray(bool useNum, bool ascOrder)
+const QuickString & KeyListOps::getOpVals(RecordKeyList &hits)
{
- if (useNum) {
- if (ascOrder) {
- sort(_numArray.begin(), _numArray.end(), less<double>());
- } else {
- sort(_numArray.begin(), _numArray.end(), greater<double>());
+ //loop through all requested columns, and for each one, call the method needed
+ //for the operation specified.
+ _methods.setKeyList(&hits);
+ _outVals.clear();
+ double val = 0.0;
+ for (int i=0; i < (int)_colOps.size(); i++) {
+ int col = _colOps[i].first;
+ OP_TYPES opCode = _colOps[i].second;
+
+ _methods.setColumn(col);
+ switch (opCode) {
+ case SUM:
+ val = _methods.getSum();
+ if (isnan(val)) {
+ _outVals.append(_methods.getNullValue());
+ } else {
+ _outVals.append(val);
+ }
+ break;
+
+ case MEAN:
+ val = _methods.getMean();
+ if (isnan(val)) {
+ _outVals.append(_methods.getNullValue());
+ } else {
+ _outVals.append(val);
+ }
+ break;
+
+ case STDDEV:
+ val = _methods.getStddev();
+ if (isnan(val)) {
+ _outVals.append(_methods.getNullValue());
+ } else {
+ _outVals.append(val);
+ }
+ break;
+
+ case SAMPLE_STDDEV:
+ val = _methods.getSampleStddev();
+ if (isnan(val)) {
+ _outVals.append(_methods.getNullValue());
+ } else {
+ _outVals.append(val);
+ }
+ break;
+
+ case MEDIAN:
+ val = _methods.getMedian();
+ if (isnan(val)) {
+ _outVals.append(_methods.getNullValue());
+ } else {
+ _outVals.append(val);
+ }
+ break;
+
+ case MODE:
+ _outVals.append(_methods.getMode());
+ break;
+
+ case ANTIMODE:
+ _outVals.append(_methods.getAntiMode());
+ break;
+
+ case MIN:
+ val = _methods.getMin();
+ if (isnan(val)) {
+ _outVals.append(_methods.getNullValue());
+ } else {
+ _outVals.append(val);
+ }
+ break;
+
+ case MAX:
+ val = _methods.getMax();
+ if (isnan(val)) {
+ _outVals.append(_methods.getNullValue());
+ } else {
+ _outVals.append(val);
+ }
+ break;
+
+ case ABSMIN:
+ val = _methods.getAbsMin();
+ if (isnan(val)) {
+ _outVals.append(_methods.getNullValue());
+ } else {
+ _outVals.append(val);
+ }
+ break;
+
+ case ABSMAX:
+ val = _methods.getAbsMax();
+ if (isnan(val)) {
+ _outVals.append(_methods.getNullValue());
+ } else {
+ _outVals.append(val);
+ }
+ break;
+
+ case COUNT:
+ _outVals.append(_methods.getCount());
+ break;
+
+ case DISTINCT:
+ _outVals.append(_methods.getDistinct());
+ break;
+
+ case COUNT_DISTINCT:
+ _outVals.append(_methods.getCountDistinct());
+ break;
+
+ case DISTINCT_ONLY:
+ _outVals.append(_methods.getDistinctOnly());
+ break;
+
+ case COLLAPSE:
+ _outVals.append(_methods.getCollapse());
+ break;
+
+ case CONCAT:
+ _outVals.append(_methods.getConcat());
+ break;
+
+ case FREQ_ASC:
+ _outVals.append(_methods.getFreqAsc());
+ break;
+
+ case FREQ_DESC:
+ _outVals.append(_methods.getFreqDesc());
+ break;
+
+ case FIRST:
+ _outVals.append(_methods.getFirst());
+ break;
+
+ case LAST:
+ _outVals.append(_methods.getLast());
+ break;
+
+ case INVALID:
+ default:
+ // Any unrecognized operation should have been handled already in the context validation.
+ // It's thus unnecessary to handle it here, but throw an error to help us know if future
+ // refactoring or code changes accidentally bypass the validation phase.
+ cerr << "ERROR: Invalid operation given for column " << col << ". Exiting..." << endl;
+ break;
}
- } else {
- if (ascOrder) {
- sort(_qsArray.begin(), _qsArray.end(), less<QuickString>());
- } else {
- sort(_qsArray.begin(), _qsArray.end(), greater<QuickString>());
+ //if this isn't the last column, add a tab.
+ if (i < (int)_colOps.size() -1) {
+ _outVals.append('\t');
}
}
+ return _outVals;
}
-void KeyListOps::makeFreqMap() {
- _freqMap.clear();
- //make a map of values to their number of times occuring.
- for (begin(); !end(); next()) {
- _freqMap[getColVal()]++;
- }
- _freqIter = _freqMap.begin();
-}
diff --git a/src/utils/KeyListOps/KeyListOps.h b/src/utils/KeyListOps/KeyListOps.h
index e294f535f54355b26b6d2ffcac7e7f0f4f78c38a..3c26d2c20b5ac49d4c608fc6ae7dd98653dfb932 100644
--- a/src/utils/KeyListOps/KeyListOps.h
+++ b/src/utils/KeyListOps/KeyListOps.h
@@ -1,117 +1,54 @@
/*
* KeyListOps.h
*
- * Created on: Feb 6, 2014
+ * Created on: Feb 24, 2014
* Author: nek3d
*/
#ifndef KEYLISTOPS_H_
#define KEYLISTOPS_H_
-using namespace std;
+#include "KeyListOpsMethods.h"
-#include <map>
-#include <utility> //for pair
-#include "QuickString.h"
-#include <stdint.h>
-#include "RecordKeyList.h"
+class FileRecordMgr;
class KeyListOps {
public:
- KeyListOps();
- KeyListOps(RecordKeyList *keyList, int column = 1);
- ~KeyListOps();
+ KeyListOps();
- void setKeyList(RecordKeyList *keyList) { _keyList = keyList; }
- void setColumn(int col) { _column = col; }
- void setNullValue(const QuickString & nullVal) { _nullVal = nullVal; }
- void setDelimStr(const QuickString &delimStr) { _delimStr = delimStr; }
+ void setColumns(const QuickString &columns) { _columns = columns; }
+ void setOperations(const QuickString & operation) { _operations = operation; }
+ void setNullValue(const QuickString & nullValue) { _methods.setNullValue(nullValue); }
+ void setDelimStr(const QuickString & delimStr) { _methods.setDelimStr(delimStr); }
+ void setKeyList(RecordKeyList *keyList) { _methods.setKeyList(keyList); }
- typedef enum { SUM, MEAN, STDDEV, SAMPLE_STDDEV, MEDIAN, MODE, ANTIMODE, MIN, MAX, ABSMIN, ABSMAX, COUNT, DISTINCT, COUNT_DISTINCT,
+ typedef enum { SUM, MEAN, STDDEV, SAMPLE_STDDEV, MEDIAN, MODE, ANTIMODE, MIN, MAX, ABSMIN, ABSMAX, COUNT, DISTINCT, COUNT_DISTINCT,
DISTINCT_ONLY, COLLAPSE, CONCAT, FREQ_ASC, FREQ_DESC, FIRST, LAST, INVALID } OP_TYPES;
- OP_TYPES getOpCode(const QuickString &operation) const;
- // return the total of the values in the vector
- double getSum();
- // return the average value in the vector
- double getMean();
- // return the standard deviation
- double getStddev();
- // return the sample standard deviation
- double getSampleStddev();
- // return the median value in the vector
- double getMedian();
- // return the most common value in the vector
- const QuickString &getMode();
- // return the least common value in the vector
- const QuickString &getAntiMode();
- // return the minimum element of the vector
- double getMin();
- // return the maximum element of the vector
- double getMax();
- // return the minimum absolute value of the vector
- double getAbsMin();
- // return the maximum absolute value of the vector
- double getAbsMax();
- // return the count of element in the vector
- uint32_t getCount();
- // return a the count of _unique_ elements in the vector
- uint32_t getCountDistinct();
- // return only those elements that occur once
- const QuickString &getDistinctOnly();
- // return a delimiter-separated list of elements
- const QuickString & getCollapse(const QuickString & delimiter = ",");
- // return a concatenation of all elements in the vector
- const QuickString & getConcat();
- // return a comma-separated list of the _unique_ elements
- const QuickString & getDistinct();
- // return a histogram of values and their freqs. in desc. order of frequency
- const QuickString & getFreqDesc();
- // return a histogram of values and their freqs. in asc. order of frequency
- const QuickString & getFreqAsc();
- // return the first value in the list
- const QuickString & getFirst();
- // return the last value in the list
- const QuickString & getLast();
-
-private:
- RecordKeyList *_keyList;
- int _column;
- QuickString _nullVal;
- QuickString _delimStr;
- QuickString _retStr;
+ bool isValidColumnOps(FileRecordMgr *dbFile);
- map<QuickString, OP_TYPES> _opCodes;
- RecordKeyList _nullKeyList; //this has to exist just so we can initialize _iter, below.
- RecordKeyList::const_iterator_type _iter;
+ const QuickString &getOpVals(RecordKeyList &hits);
- // Some methods need to put values into a vector, mostly for sorting.
- vector<double> _numArray;
- vector<QuickString> _qsArray;
+private:
+ void init();
- typedef map<QuickString, int> freqMapType;
- freqMapType _freqMap;
- freqMapType::iterator _freqIter;
+ QuickString _operations;
+ QuickString _columns;
- typedef enum { UNSORTED, ASC, DESC} SORT_TYPE;
+ KeyListOpsMethods _methods;
+ map<QuickString, OP_TYPES> _opCodes;
+ map<OP_TYPES, bool> _isNumericOp;
- typedef multimap<int, QuickString, less<int> > histAscType;
- typedef multimap<int, QuickString, greater<int> > histDescType;
- void init();
- const QuickString &getColVal();
- double getColValNum();
- bool empty() { return _keyList->empty(); }
- void begin() { _iter = _keyList->begin(); }
- bool end() { return _iter == _keyList->end(); }
- void next() { _iter = _keyList->next(); }
- void toArray(bool useNum, SORT_TYPE sortVal = UNSORTED);
- void sortArray(bool useNum, bool ascOrder);
- void makeFreqMap();
+ typedef vector<pair<int, OP_TYPES> > colOpsType;
+ colOpsType _colOps;
+ QuickString _outVals;
+ OP_TYPES getOpCode(const QuickString &operation) const;
+ bool isNumericOp(OP_TYPES op) const;
+ bool isNumericOp(const QuickString &op) const;
};
-
#endif /* KEYLISTOPS_H_ */
diff --git a/src/utils/KeyListOps/KeyListOpsMethods.cpp b/src/utils/KeyListOps/KeyListOpsMethods.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..0b0013582ee059f3f564a2788a455b4527ddef46
--- /dev/null
+++ b/src/utils/KeyListOps/KeyListOpsMethods.cpp
@@ -0,0 +1,368 @@
+/*
+ * KeyListOpsMethods.cpp
+ *
+ * Created on: Feb 6, 2014
+ * Author: nek3d
+ */
+
+#include "KeyListOpsMethods.h"
+#include <cfloat>
+#include <cmath>
+#include <algorithm>
+
+KeyListOpsMethods::KeyListOpsMethods()
+: _keyList(&_nullKeyList),
+ _column(1),
+ _nullVal("."),
+ _delimStr(","),
+ _iter(_nullKeyList.begin())
+{
+}
+
+KeyListOpsMethods::KeyListOpsMethods(RecordKeyList *keyList, int column)
+: _keyList(keyList),
+ _column(column),
+ _nullVal("."),
+ _delimStr(","),
+ _iter(keyList->begin())
+{
+}
+
+
+KeyListOpsMethods::~KeyListOpsMethods() {
+
+}
+
+// return the total of the values in the vector
+double KeyListOpsMethods::getSum() {
+ if (empty()) return NAN;
+
+ double theSum = 0.0;
+ for (begin(); !end(); next()) {
+ theSum += getColValNum();
+ }
+ return theSum;
+}
+
+// return the average value in the vector
+double KeyListOpsMethods::getMean() {
+ if (empty()) return NAN;
+
+ return getSum() / (float)getCount();
+}
+
+
+ // return the standard deviation
+double KeyListOpsMethods::getStddev() {
+ if (empty()) return NAN;
+
+ double avg = getMean();
+ double squareDiffSum = 0.0;
+ for (begin(); !end(); next()) {
+ double val = getColValNum();
+ double diff = val - avg;
+ squareDiffSum += diff * diff;
+ }
+ return squareDiffSum / (float)getCount();
+}
+// return the standard deviation
+double KeyListOpsMethods::getSampleStddev() {
+ if (empty()) return NAN;
+
+ double avg = getMean();
+ double squareDiffSum = 0.0;
+ for (begin(); !end(); next()) {
+ double val = getColValNum();
+ double diff = val - avg;
+ squareDiffSum += diff * diff;
+ }
+ return squareDiffSum / ((float)getCount() - 1.0);
+}
+
+// return the median value in the vector
+double KeyListOpsMethods::getMedian() {
+ if (empty()) return NAN;
+
+ //get sorted vector. if even number of elems, return middle val.
+ //if odd, average of two.
+ toArray(true, ASC);
+ size_t count = getCount();
+ if (count % 2) {
+ //odd number of elements. Take middle one.
+ return _numArray[count/2];
+ } else {
+ //even numnber of elements. Take average of middle 2.
+ double sum = _numArray[count/2 -1] + _numArray[count/2];
+ return sum / 2.0;
+ }
+}
+
+// return the most common value in the vector
+const QuickString &KeyListOpsMethods::getMode() {
+ if (empty()) return _nullVal;
+
+ makeFreqMap();
+
+ //now pass through the freq map and keep track of which key has the highest occurance.
+ freqMapType::iterator maxIter = _freqMap.begin();
+ int maxVal = 0;
+ for (; _freqIter != _freqMap.end(); _freqIter++) {
+ if (_freqIter->second > maxVal) {
+ maxIter = _freqIter;
+ maxVal = _freqIter->second;
+ }
+ }
+ _retStr = maxIter->first;
+ return _retStr;
+}
+// return the least common value in the vector
+const QuickString &KeyListOpsMethods::getAntiMode() {
+ if (empty()) return _nullVal;
+
+ makeFreqMap();
+
+ //now pass through the freq map and keep track of which key has the highest occurance.
+ freqMapType::iterator minIter = _freqMap.begin();
+ int minVal = INT_MAX;
+ for (; _freqIter != _freqMap.end(); _freqIter++) {
+ if (_freqIter->second < minVal) {
+ minIter = _freqIter;
+ minVal = _freqIter->second;
+ }
+ }
+ _retStr = minIter->first;
+ return _retStr;
+}
+// return the minimum element of the vector
+double KeyListOpsMethods::getMin() {
+ if (empty()) return NAN;
+
+ double minVal = DBL_MAX;
+ for (begin(); !end(); next()) {
+ double currVal = getColValNum();
+ minVal = (currVal < minVal) ? currVal : minVal;
+ }
+ return minVal;
+}
+
+// return the maximum element of the vector
+double KeyListOpsMethods::getMax() {
+ if (empty()) return NAN;
+
+ double maxVal = DBL_MIN;
+ for (begin(); !end(); next()) {
+ double currVal = getColValNum();
+ maxVal = (currVal > maxVal) ? currVal : maxVal;
+ }
+ return maxVal;
+}
+
+// return the minimum absolute value of the vector
+double KeyListOpsMethods::getAbsMin() {
+ if (empty()) return NAN;
+
+ double minVal = DBL_MAX;
+ for (begin(); !end(); next()) {
+ double currVal = abs(getColValNum());
+ minVal = (currVal < minVal) ? currVal : minVal;
+ }
+ return minVal;
+}
+// return the maximum absolute value of the vector
+double KeyListOpsMethods::getAbsMax() {
+ if (empty()) return NAN;
+
+ double maxVal = DBL_MIN;
+ for (begin(); !end(); next()) {
+ double currVal = abs(getColValNum());
+ maxVal = (currVal > maxVal) ? currVal : maxVal;
+ }
+ return maxVal;
+}
+// return the count of element in the vector
+uint32_t KeyListOpsMethods::getCount() {
+ return _keyList->size();
+}
+// return a delimited list of the unique elements
+const QuickString &KeyListOpsMethods::getDistinct() {
+ if (empty()) return _nullVal;
+ // separated list of unique values. If something repeats, only report once.
+ makeFreqMap();
+ _retStr.clear();
+ for (; _freqIter != _freqMap.end(); _freqIter++) {
+ if (_freqIter != _freqMap.begin()) _retStr += _delimStr;
+ _retStr.append(_freqIter->first);
+ }
+ return _retStr;
+}
+
+const QuickString &KeyListOpsMethods::getDistinctOnly() {
+ if (empty()) return _nullVal;
+
+ //separated list of only unique values. If item repeats, discard.
+ makeFreqMap();
+ _retStr.clear();
+ for (; _freqIter != _freqMap.end(); _freqIter++) {
+ if (_freqIter->second != 1) continue;
+ if (_freqIter != _freqMap.begin()) _retStr += _delimStr;
+ _retStr.append(_freqIter->first);
+ }
+ return _retStr;
+}
+
+// return a the count of _unique_ elements in the vector
+uint32_t KeyListOpsMethods::getCountDistinct() {
+ if (empty()) return 0;
+
+ makeFreqMap();
+ return _freqMap.size();
+}
+// return a delimiter-separated list of elements
+const QuickString &KeyListOpsMethods::getCollapse(const QuickString &delimiter) {
+ if (empty()) return _nullVal;
+
+ //just put all items in one big separated list.
+ _retStr.clear();
+ int i=0;
+ for (begin(); !end(); next()) {
+ if (i > 0) _retStr += _delimStr;
+ _retStr.append(getColVal());
+ i++;
+ }
+ return _retStr;
+
+}
+// return a concatenation of all elements in the vector
+const QuickString &KeyListOpsMethods::getConcat() {
+ if (empty()) return _nullVal;
+
+ //like collapse but w/o commas. Just a true concat of all vals.
+ //just swap out the delimChar with '' and call collapse, then
+ //restore the delimChar.
+ QuickString oldDelimStr(_delimStr);
+ _delimStr = "";
+ getCollapse(); //this will store it's results in the _retStr method.
+ _delimStr = oldDelimStr;
+ return _retStr;
+}
+
+// return a histogram of values and their freqs. in desc. order of frequency
+const QuickString &KeyListOpsMethods::getFreqDesc() {
+ if (empty()) return _nullVal;
+
+ //for each uniq val, report # occurances, in desc order.
+ makeFreqMap();
+ //put freq map into multimap where key is the freq and val is the item. In other words, basically a reverse freq map.
+ histDescType hist;
+ for (; _freqIter != _freqMap.end(); _freqIter++) {
+ hist.insert(pair<int, QuickString>(_freqIter->second, _freqIter->first));
+ }
+ //now iterate through the reverse map we just made and output it's pairs in val:key format.
+ _retStr.clear();
+ for (histDescType::iterator histIter = hist.begin(); histIter != hist.end(); histIter++) {
+ if (histIter != hist.begin()) _retStr += _delimStr;
+ _retStr.append(histIter->second);
+ _retStr += ":";
+ _retStr.append(histIter->first);
+ }
+ return _retStr;
+}
+// return a histogram of values and their freqs. in asc. order of frequency
+const QuickString &KeyListOpsMethods::getFreqAsc() {
+ if (empty()) return _nullVal;
+
+ //for each uniq val, report # occurances, in asc order.
+ makeFreqMap();
+ //put freq map into multimap where key is the freq and val is the item. In other words, basically a reverse freq map.
+ histAscType hist;
+ for (; _freqIter != _freqMap.end(); _freqIter++) {
+ hist.insert(pair<int, QuickString>(_freqIter->second, _freqIter->first));
+// hist[*(_freqIter->second)] = _freqIter->first;
+ }
+ //now iterate through the reverse map we just made and output it's pairs in val:key format.
+ _retStr.clear();
+ for (histAscType::iterator histIter = hist.begin(); histIter != hist.end(); histIter++) {
+ if (histIter != hist.begin()) _retStr += _delimStr;
+ _retStr.append(histIter->second);
+ _retStr += ":";
+ _retStr.append(histIter->first);
+ }
+ return _retStr;
+}
+// return the first value in the list
+const QuickString &KeyListOpsMethods::getFirst() {
+ if (empty()) return _nullVal;
+
+ //just the first item.
+ begin();
+ return getColVal();
+}
+// return the last value in the list
+const QuickString &KeyListOpsMethods::getLast() {
+ if (empty()) return _nullVal;
+
+ //just the last item.
+ begin();
+ for (size_t i = 0; i < getCount() -1; i++) {
+ next();
+ }
+ return getColVal();
+}
+
+const QuickString &KeyListOpsMethods::getColVal() {
+ return _iter->value()->getField(_column);
+}
+
+double KeyListOpsMethods::getColValNum() {
+ return atof(_iter->value()->getField(_column).c_str());
+}
+
+void KeyListOpsMethods::toArray(bool useNum, SORT_TYPE sortVal) {
+
+ //TBD: optimize performance with better memory management.
+ if (useNum) {
+ _numArray.resize(_keyList->size());
+ int i=0;
+ for (begin(); !end(); next()) {
+ _numArray[i] = getColValNum();
+ i++;
+ }
+ } else {
+ _qsArray.resize(_keyList->size());
+ int i=0;
+ for (begin(); !end(); next()) {
+ _qsArray[i] = getColVal();
+ i++;
+ }
+ }
+ if (sortVal != UNSORTED) {
+ sortArray(useNum, sortVal == ASC);
+ }
+}
+
+void KeyListOpsMethods::sortArray(bool useNum, bool ascOrder)
+{
+ if (useNum) {
+ if (ascOrder) {
+ sort(_numArray.begin(), _numArray.end(), less<double>());
+ } else {
+ sort(_numArray.begin(), _numArray.end(), greater<double>());
+ }
+ } else {
+ if (ascOrder) {
+ sort(_qsArray.begin(), _qsArray.end(), less<QuickString>());
+ } else {
+ sort(_qsArray.begin(), _qsArray.end(), greater<QuickString>());
+ }
+ }
+}
+
+void KeyListOpsMethods::makeFreqMap() {
+ _freqMap.clear();
+
+ //make a map of values to their number of times occuring.
+ for (begin(); !end(); next()) {
+ _freqMap[getColVal()]++;
+ }
+ _freqIter = _freqMap.begin();
+}
diff --git a/src/utils/KeyListOps/KeyListOpsMethods.h b/src/utils/KeyListOps/KeyListOpsMethods.h
new file mode 100644
index 0000000000000000000000000000000000000000..0cac9c87a196cd3107dd953e7710e637205d2125
--- /dev/null
+++ b/src/utils/KeyListOps/KeyListOpsMethods.h
@@ -0,0 +1,113 @@
+/*
+ * KeyListOpsMethods.h
+ *
+ * Created on: Feb 6, 2014
+ * Author: nek3d
+ */
+
+#ifndef KEYLISTOPSMETHODS_H_
+#define KEYLISTOPSMETHODS_H_
+
+using namespace std;
+
+#include <map>
+#include <utility> //for pair
+#include "QuickString.h"
+#include <stdint.h>
+#include "RecordKeyList.h"
+
+class KeyListOpsMethods {
+public:
+ KeyListOpsMethods();
+ KeyListOpsMethods(RecordKeyList *keyList, int column = 1);
+ ~KeyListOpsMethods();
+
+
+ void setKeyList(RecordKeyList *keyList) { _keyList = keyList; }
+ void setColumn(int col) { _column = col; }
+ void setNullValue(const QuickString & nullVal) { _nullVal = nullVal; }
+ const QuickString &getNullValue() const { return _nullVal; }
+ void setDelimStr(const QuickString &delimStr) { _delimStr = delimStr; }
+ const QuickString &getDelimStr() const { return _delimStr; }
+
+ // return the total of the values in the vector
+ double getSum();
+ // return the average value in the vector
+ double getMean();
+ // return the standard deviation
+ double getStddev();
+ // return the sample standard deviation
+ double getSampleStddev();
+ // return the median value in the vector
+ double getMedian();
+ // return the most common value in the vector
+ const QuickString &getMode();
+ // return the least common value in the vector
+ const QuickString &getAntiMode();
+ // return the minimum element of the vector
+ double getMin();
+ // return the maximum element of the vector
+ double getMax();
+ // return the minimum absolute value of the vector
+ double getAbsMin();
+ // return the maximum absolute value of the vector
+ double getAbsMax();
+ // return the count of element in the vector
+ uint32_t getCount();
+ // return a the count of _unique_ elements in the vector
+ uint32_t getCountDistinct();
+ // return only those elements that occur once
+ const QuickString &getDistinctOnly();
+ // return a delimiter-separated list of elements
+ const QuickString & getCollapse(const QuickString & delimiter = ",");
+ // return a concatenation of all elements in the vector
+ const QuickString & getConcat();
+ // return a comma-separated list of the _unique_ elements
+ const QuickString & getDistinct();
+ // return a histogram of values and their freqs. in desc. order of frequency
+ const QuickString & getFreqDesc();
+ // return a histogram of values and their freqs. in asc. order of frequency
+ const QuickString & getFreqAsc();
+ // return the first value in the list
+ const QuickString & getFirst();
+ // return the last value in the list
+ const QuickString & getLast();
+
+private:
+ RecordKeyList *_keyList;
+ int _column;
+ QuickString _nullVal;
+ QuickString _delimStr;
+ QuickString _retStr;
+
+ RecordKeyList _nullKeyList; //this has to exist just so we can initialize _iter, below.
+ RecordKeyList::const_iterator_type _iter;
+
+ // Some methods need to put values into a vector, mostly for sorting.
+ vector<double> _numArray;
+ vector<QuickString> _qsArray;
+
+ typedef map<QuickString, int> freqMapType;
+ freqMapType _freqMap;
+ freqMapType::iterator _freqIter;
+
+ typedef enum { UNSORTED, ASC, DESC} SORT_TYPE;
+
+ typedef multimap<int, QuickString, less<int> > histAscType;
+ typedef multimap<int, QuickString, greater<int> > histDescType;
+ void init();
+ const QuickString &getColVal();
+ double getColValNum();
+ bool empty() { return _keyList->empty(); }
+ void begin() { _iter = _keyList->begin(); }
+ bool end() { return _iter == _keyList->end(); }
+ void next() { _iter = _keyList->next(); }
+ void toArray(bool useNum, SORT_TYPE sortVal = UNSORTED);
+ void sortArray(bool useNum, bool ascOrder);
+ void makeFreqMap();
+
+
+};
+
+
+#endif /* KEYLISTOPSMETHODS_H_ */
diff --git a/src/utils/KeyListOps/Makefile b/src/utils/KeyListOps/Makefile
index 1797c83985ea50a7bec3979819b27cbd11d0b742..0b0ac991d175b7bcf24999bed1131a6a2aed2b4a 100644
--- a/src/utils/KeyListOps/Makefile
+++ b/src/utils/KeyListOps/Makefile
@@ -6,7 +6,6 @@ UTILITIES_DIR = ../../utils/
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/general/ \
-I$(UTILITIES_DIR)/fileType/ \
- -I$(UTILITIES_DIR)/Contexts/ \
-I$(UTILITIES_DIR)/GenomeFile/ \
-I$(UTILITIES_DIR)/FileRecordTools/ \
-I$(UTILITIES_DIR)/FileRecordTools/FileReaders/ \
@@ -19,21 +18,26 @@ INCLUDES = -I$(UTILITIES_DIR)/general/ \
# ----------------------------------
# define our source and object files
# ----------------------------------
-SOURCES= KeyListOps.cpp KeyListOps.h
-OBJECTS= KeyListOps.o
+SOURCES= KeyListOps.cpp KeyListOps.h KeyListOpsMethods.cpp KeyListOpsMethods.h
+OBJECTS= KeyListOps.o KeyListOpsMethods.o
_EXT_OBJECTS=
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
+all: $(BUILT_OBJECTS)
+
+.PHONY: all
+
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+
$(EXT_OBJECTS):
@$(MAKE) --no-print-directory -C $(INCLUDES)
clean:
@echo "Cleaning up."
- @rm -f $(OBJ_DIR)/KeyListOps.o
+ @rm -f $(OBJ_DIR)/KeyListOps.o $(OBJ_DIR)/KeyListOpsMethods.o
.PHONY: clean
\ No newline at end of file
diff --git a/src/utils/NewChromsweep/Makefile b/src/utils/NewChromsweep/Makefile
index 8f4d93105b30488d40a10599c2d1bd0b083576cf..34fc5d1234a527b470e7b606faa87c0adaf9f0e8 100644
--- a/src/utils/NewChromsweep/Makefile
+++ b/src/utils/NewChromsweep/Makefile
@@ -11,6 +11,7 @@ INCLUDES = -I$(UTILITIES_DIR)/general/ \
-I$(UTILITIES_DIR)/FileRecordTools/ \
-I$(UTILITIES_DIR)/FileRecordTools/FileReaders/ \
-I$(UTILITIES_DIR)/FileRecordTools/Records/ \
+ -I$(UTILITIES_DIR)/KeyListOps/ \
-I$(UTILITIES_DIR)/BamTools/include \
-I$(UTILITIES_DIR)/BamTools/src/ \
-I$(UTILITIES_DIR)/version/
diff --git a/src/utils/RecordOutputMgr/Makefile b/src/utils/RecordOutputMgr/Makefile
index 2d196ec11518d10b6f57877c77bc35b7b9063446..346a5c7caf02bb7855164d671221801308e97d9e 100644
--- a/src/utils/RecordOutputMgr/Makefile
+++ b/src/utils/RecordOutputMgr/Makefile
@@ -11,6 +11,7 @@ INCLUDES = -I$(UTILITIES_DIR)/general/ \
-I$(UTILITIES_DIR)/FileRecordTools/ \
-I$(UTILITIES_DIR)/FileRecordTools/FileReaders/ \
-I$(UTILITIES_DIR)/FileRecordTools/Records/ \
+ -I$(UTILITIES_DIR)/KeyListOps/ \
-I$(UTILITIES_DIR)/BamTools/include \
-I$(UTILITIES_DIR)/BamTools/src/ \
-I$(UTILITIES_DIR)/version/
diff --git a/test/map/test-map.sh b/test/map/test-map.sh
index f62d364207c2612a368a30a513f0e5c9ff1462c6..d9ecbaca890ad1c25b567b97b8c42a0c9cb26604 100644
--- a/test/map/test-map.sh
+++ b/test/map/test-map.sh
@@ -656,7 +656,7 @@ rm obs exp
# Test that Bam database is not allowed
############################################################
echo " map.t44...\c"
-echo -e "\n*****\n***** ERROR: BAM database file not currently supported for the map tool." > exp
+echo -e "\n*****\n***** ERROR: BAM database file not currently supported for column operations." > exp
$BT map -a ivls.bed -b values.bam 2> obs
check obs exp
rm obs exp
@@ -671,3 +671,122 @@ echo "chr1 0 50 three_blocks_match 15 + 0 0 0 3 10,10,10, 0,20,40, ." > exp
$BT map -o sum -a three_blocks_match.bed -b three_blocks_nomatch.bed -split > obs
check obs exp
rm obs exp
+
+
+
+
+
+
+###########################################################
+#
+#
+# Tests for multiple columns and operations
+#
+#
+############################################################
+
+
+###########################################################
+# Test that error is given when ops outnumber columns
+############################################################
+echo " map.t46...\c"
+echo \
+"
+*****
+***** ERROR: There are 1 columns given, but there are 2 operations." > exp
+../../bin/bedtools map -a ivls.bed -b values.bed -o count,sum 2>&1 > /dev/null | head -3 > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test that error is given when columns outnumber ops,
+# if there are two or more ops.
+############################################################
+echo " map.t47...\c"
+echo \
+"
+*****
+***** ERROR: There are 3 columns given, but there are 2 operations." > exp
+../../bin/bedtools map -a ivls.bed -b values.bed -c 5,1,2 -o count,sum 2>&1 > /dev/null | head -3 > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test that numeric ops for non-numeric columns aren't allowed
+############################################################
+echo " map.t48...\c"
+echo \
+"
+*****
+***** ERROR: Column 1 is not a numeric field for database file values.bed." > exp
+../../bin/bedtools map -a ivls.bed -b values.bed -c 1 -o sum 2>&1 > /dev/null | head -3 > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test that multiple columns are allowed with a
+# single operation
+############################################################
+echo " map.t49...\c"
+echo \
+"chr1 0 100 65 9
+chr1 100 200 1 7
+chr2 0 100 . .
+chr2 100 200 . .
+chr3 0 100 6 7
+chr3 100 200 8 23" > exp
+../../bin/bedtools map -a ivls.bed -b values4.bed -c 5,7 -o sum > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test that multiple columns are allowed with an
+# equal number of ops that aren't all the same
+############################################################
+echo " map.t50...\c"
+echo \
+"chr1 0 100 13.5 65 9
+chr1 100 200 120 1 7
+chr2 0 100 . . .
+chr2 100 200 . . .
+chr3 0 100 10 6 7
+chr3 100 200 120 8 23" > exp
+../../bin/bedtools map -a ivls.bed -b values4.bed -c 2,5,7 -o mean,sum,sum > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test stddev
+############################################################
+echo " map.t51...\c"
+echo \
+"chr1 0 100 12.9167
+chr1 100 200 0
+chr2 0 100 .
+chr2 100 200 .
+chr3 0 100 76.2222
+chr3 100 200 0.25" > exp
+../../bin/bedtools map -a ivls.bed -b values4.bed -c 7 -o stddev > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# Test sample_stddev
+############################################################
+echo " map.t52...\c"
+echo \
+"chr1 0 100 15.5
+chr1 100 200 .
+chr2 0 100 .
+chr2 100 200 .
+chr3 0 100 114.333
+chr3 100 200 0.5" > exp
+../../bin/bedtools map -a ivls.bed -b values4.bed -c 7 -o sample_stddev > obs
+check obs exp
+rm obs exp
+