From 8219b6d93bd82ea065ae7c6e5589c580fea1b96f Mon Sep 17 00:00:00 2001
From: nkindlon <nek3d@virginia.edu>
Date: Thu, 19 Sep 2013 18:21:14 -0400
Subject: [PATCH] Improved help and error msgs in Context
---
src/intersectFile/intersectMain.cpp | 4 ++--
src/utils/Contexts/Context.cpp | 34 ++++++++++++++++++++++++++---
src/utils/Contexts/Context.h | 3 ++-
3 files changed, 35 insertions(+), 6 deletions(-)
diff --git a/src/intersectFile/intersectMain.cpp b/src/intersectFile/intersectMain.cpp
index 9fcb8a1b..a220b24f 100644
--- a/src/intersectFile/intersectMain.cpp
+++ b/src/intersectFile/intersectMain.cpp
@@ -23,8 +23,8 @@ void intersect_help(void);
int intersect_main(int argc, char* argv[]) {
Context *context = new Context();
- context->parseCmdArgs(argc, argv, 1);
- if (context->getShowHelp() || !context->isValidState()) {
+
+ if (!context->parseCmdArgs(argc, argv, 1) || context->getShowHelp() || !context->isValidState()) {
if (!context->getErrorMsg().empty()) {
cerr << context->getErrorMsg() << endl;
}
diff --git a/src/utils/Contexts/Context.cpp b/src/utils/Contexts/Context.cpp
index 97143c22..6b858065 100644
--- a/src/utils/Contexts/Context.cpp
+++ b/src/utils/Contexts/Context.cpp
@@ -44,6 +44,8 @@ Context::Context()
_reportNames(false),
_reportScores(false)
{
+ _programNames["intersect"] = INTERSECT;
+
_validScoreOps.insert("sum");
_validScoreOps.insert("max");
_validScoreOps.insert("min");
@@ -90,15 +92,17 @@ void Context::openGenomeFile(const BamTools::RefVector &refVector)
_genomeFile = new NewGenomeFile(refVector);
}
-void Context::parseCmdArgs(int argc, char **argv, int skipFirstArgs) {
+bool Context::parseCmdArgs(int argc, char **argv, int skipFirstArgs) {
_argc = argc;
_argv = argv;
_skipFirstArgs = skipFirstArgs;
if (argc < 2) {
setShowHelp(true);
- return;
+ return false;
}
+ setProgram(_programNames[argv[0]]);
+
_argsProcessed.resize(argc - skipFirstArgs, false);
for (int i=skipFirstArgs; i < argc; i++) {
@@ -112,6 +116,10 @@ void Context::parseCmdArgs(int argc, char **argv, int skipFirstArgs) {
i++;
markUsed(i - skipFirstArgs);
} else if (strcmp(argv[i], "-g") == 0) {
+ if (argc <= i+1) {
+ _errorMsg = "Error: -g option given, but no genome file specified.";
+ return false;
+ }
openGenomeFile(argv[i+1]);
markUsed(i - skipFirstArgs);
i++;
@@ -128,6 +136,11 @@ void Context::parseCmdArgs(int argc, char **argv, int skipFirstArgs) {
markUsed(i - skipFirstArgs);
}
if (strcmp(argv[i], "-a") == 0) {
+ if (argc <= i+1) {
+ _errorMsg = "Error: -a option given, but no query file specified.";
+ return false;
+ }
+
addInputFile(argv[i+1]);
_queryFileIdx = getNumInputFiles() -1;
markUsed(i - skipFirstArgs);
@@ -135,6 +148,10 @@ void Context::parseCmdArgs(int argc, char **argv, int skipFirstArgs) {
markUsed(i - skipFirstArgs);
}
else if(strcmp(argv[i], "-abam") == 0) {
+ if (argc <= i+1) {
+ _errorMsg = "Error: -abam option given, but no query BAM file specified.";
+ return false;
+ }
addInputFile(argv[i+1]);
_queryFileIdx = getNumInputFiles() -1;
markUsed(i - skipFirstArgs);
@@ -143,6 +160,10 @@ void Context::parseCmdArgs(int argc, char **argv, int skipFirstArgs) {
setInputFileType(_queryFileIdx, FileRecordTypeChecker::BAM_FILE_TYPE);
}
else if (strcmp(argv[i], "-b") == 0) {
+ if (argc <= i+1) {
+ _errorMsg = "Error: -b option given, but no database file specified.";
+ return false;
+ }
addInputFile(argv[i+1]);
_databaseFileIdx = getNumInputFiles() -1;
markUsed(i - skipFirstArgs);
@@ -218,13 +239,20 @@ void Context::parseCmdArgs(int argc, char **argv, int skipFirstArgs) {
markUsed(i - skipFirstArgs);
}
}
+ return true;
}
bool Context::isValidState()
{
- if (!Context::cmdArgsValid()) {
+ if (!cmdArgsValid()) {
return false;
}
+
+ if (getProgram() == INTERSECT && (_queryFileIdx == -1 || _databaseFileIdx == -1)) {
+ _errorMsg = "Error: Intersect program was not given a query and database file.";
+ return false;
+ }
+
if (getAnyHit() && getNoHit()) {
_errorMsg = "Error: request either -u for anyHit OR -v for noHit, not both.";
return false;
diff --git a/src/utils/Contexts/Context.h b/src/utils/Contexts/Context.h
index f65528d0..5638e087 100644
--- a/src/utils/Contexts/Context.h
+++ b/src/utils/Contexts/Context.h
@@ -74,7 +74,7 @@ public:
void setOutputFileType(ContextFileType fileType) { _outputFileType = fileType; }
ContextFileType getOutputFileType() const { return _outputFileType; }
- void parseCmdArgs(int argc, char **argv, int skipFirstArgs);
+ bool parseCmdArgs(int argc, char **argv, int skipFirstArgs);
//isValidState checks that parameters to context are in an acceptable state.
// If not, the error msg string will be set with a reason why it failed.
@@ -193,6 +193,7 @@ protected:
ContextRecordType _recordType;
};
vector<FileEntryType> _inputFiles;
+ map<QuickString, PROGRAM_TYPE> _programNames;
bool _useMergedIntervals;
NewGenomeFile *_genomeFile;
--
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