From ebf9a72ce28b208fd512e7efb5a3851e8bf8bc76 Mon Sep 17 00:00:00 2001
From: arq5x <arq5x@virginia.edu>
Date: Sat, 1 Feb 2014 16:44:14 -0500
Subject: [PATCH] add a Context for Map tool.
---
src/utils/Contexts/ContextMap.cpp | 121 ++++++++++++++++++++++++++++++
src/utils/Contexts/ContextMap.h | 39 ++++++++++
2 files changed, 160 insertions(+)
create mode 100644 src/utils/Contexts/ContextMap.cpp
create mode 100644 src/utils/Contexts/ContextMap.h
diff --git a/src/utils/Contexts/ContextMap.cpp b/src/utils/Contexts/ContextMap.cpp
new file mode 100644
index 00000000..80fd2b7b
--- /dev/null
+++ b/src/utils/Contexts/ContextMap.cpp
@@ -0,0 +1,121 @@
+/*
+ * ContextMap.cpp
+ *
+ * Created on: Jan 6, 2014
+ * Author: arq5x
+ */
+
+#include "ContextMap.h"
+
+ContextMap::ContextMap()
+{
+ // map requires sorted input
+ setSortedInput(true);
+ setLeftJoin(true);
+
+ // default to BED score column
+ setColumn(5);
+ // default to "sum"
+ setColumnOperation("sum");
+ // default to "." as a NULL value
+ setNullValue('.');
+}
+
+ContextMap::~ContextMap()
+{
+
+}
+
+
+bool ContextMap::parseCmdArgs(int argc, char **argv, int skipFirstArgs) {
+ _argc = argc;
+ _argv = argv;
+ _skipFirstArgs = skipFirstArgs;
+ if (_argc < 2) {
+ setShowHelp(true);
+ return false;
+ }
+
+ setProgram(_programNames[argv[0]]);
+
+ _argsProcessed.resize(_argc - _skipFirstArgs, false);
+
+ for (_i=_skipFirstArgs; _i < argc; _i++) {
+ 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;
+ }
+ }
+ return ContextIntersect::parseCmdArgs(argc, argv, _skipFirstArgs);
+}
+
+
+bool ContextMap::isValidState()
+{
+ if (!cmdArgsValid()) {
+ return false;
+ }
+
+ ContextIntersect::isValidState();
+
+ 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);
+ }
+ // TODO
+ // enforce any specific checks for Map.
+
+ return ContextIntersect::isValidState();
+}
+
+
+// for map, -c is the column upon which to operate
+bool ContextMap::handle_c()
+{
+ if ((_i+1) < _argc) {
+ setColumn(atoi(_argv[_i + 1]));
+ markUsed(_i - _skipFirstArgs);
+ _i++;
+ markUsed(_i - _skipFirstArgs);
+ }
+ return true;
+}
+
+
+// for map, -o is the operation to apply to the column (-c)
+bool ContextMap::handle_o()
+{
+ if ((_i+1) < _argc) {
+ setColumnOperation(_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;
+}
diff --git a/src/utils/Contexts/ContextMap.h b/src/utils/Contexts/ContextMap.h
new file mode 100644
index 00000000..b8ee57fd
--- /dev/null
+++ b/src/utils/Contexts/ContextMap.h
@@ -0,0 +1,39 @@
+/*
+ * ContextMap.h
+ *
+ * Created on: Jan 7, 2014
+ * Author: arq5x
+ */
+
+#ifndef CONTEXTMAP_H_
+#define CONTEXTMAP_H_
+
+#include "ContextIntersect.h"
+
+class ContextMap : public ContextIntersect {
+public:
+ ContextMap();
+ virtual ~ContextMap();
+ virtual bool isValidState();
+
+ virtual bool parseCmdArgs(int argc, char **argv, int skipFirstArgs);
+
+ int getColumn() const { return _column; }
+ void setColumn(int column) { _column = column; }
+
+ const QuickString & getColumnOperation() const { return _columnOperation; }
+ void setColumnOperation(const QuickString & operation) { _columnOperation = operation; }
+
+ const QuickString & getNullValue() const { return _nullValue; }
+ void setNullValue(const QuickString & nullValue) { _nullValue = nullValue; }
+
+ virtual bool hasIntersectMethods() const { return true; }
+
+private:
+ virtual bool handle_c();
+ virtual bool handle_o();
+ virtual bool handle_null();
+
+};
+
+#endif /* CONTEXTMAP_H_ */
--
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