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/*
* ContextMerge.cpp
*
* Created on: Mar 26, 2014
* Author: nek3d
*/
#include "ContextMerge.h"
ContextMerge::ContextMerge()
{
setUseMergedIntervals(true);
setColumnOpsMethods(true);
//merge has no default columnOps the way map does, so we'll need to clear those.
_keyListOps->setColumns("");
_keyListOps->setOperations("");
}
ContextMerge::~ContextMerge()
{
}
bool ContextMerge::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], "-n") == 0) {
if (!handle_n()) return false;
}
else if (strcmp(_argv[_i], "-nms") == 0) {
if (!handle_nms()) return false;
}
else if (strcmp(_argv[_i], "-scores") == 0) {
if (!handle_scores()) return false;
}
else if (strcmp(_argv[_i], "-delim") == 0) {
if (!handle_delim()) return false;
}
else if (strcmp(_argv[_i], "-d") == 0) {
if (!handle_d()) return false;
}
else if (strcmp(_argv[_i], "-s") == 0) {
if (!handle_s()) return false;
}
else if (strcmp(_argv[_i], "-S") == 0) {
if (!handle_S()) return false;
}
}
return ContextBase::parseCmdArgs(argc, argv, _skipFirstArgs);
}
bool ContextMerge::isValidState()
{
// Special: The merge program does not have default
//column operations, so if none were entered, disable column ops.
if (_keyListOps->getColumns().empty() && _keyListOps->getOperations().empty()) {
setColumnOpsMethods(false);
delete _keyListOps;
_keyListOps = NULL;
}
if (!ContextBase::isValidState()) {
return false;
}
if (_files.size() != 1) {
_errorMsg = "\n***** ERROR: input file not specified. *****";
// Allow one and only input file for now
return false;
}
return true;
}
bool ContextMerge::handle_d() {
if ((_i+1) < _argc) {
if (isNumeric(_argv[_i+1])) {
int dist = str2chrPos(_argv[_i+1]);
if (dist >=0 ) {
_maxDistance = dist;
markUsed(_i - _skipFirstArgs);
_i++;
markUsed(_i - _skipFirstArgs);
return true;
}
}
}
_errorMsg = "\n***** ERROR: -d option must be followed by an integer value *****";
return false;
}
bool ContextMerge::handle_n()
{
//This is the same as telling map "-c any -o count"
_keyListOps->addColumns("1"); //doesn't really matter which column, but the default column
//for keyListOps is score, which not every record necessarily has.
_keyListOps->addOperations("count");
markUsed(_i - _skipFirstArgs);
return true;
}
bool ContextMerge::handle_nms()
{
//This is the same as telling map "-c 4 -o collapse"
_keyListOps->addColumns("4");
_keyListOps->addOperations("collapse");
markUsed(_i - _skipFirstArgs);
return true;
}
bool ContextMerge::handle_scores()
{
if ((_i+1) < _argc) {
_keyListOps->addColumns("5");
_keyListOps->addOperations(_argv[_i+1]);
markUsed(_i - _skipFirstArgs);
_i++;
markUsed(_i - _skipFirstArgs);
return true;
}
_errorMsg = "\n***** ERROR: -scores option given, but no operation specified. *****";
return false;
}
bool ContextMerge::handle_s() {
_desiredStrand = FileRecordMergeMgr::SAME_STRAND_EITHER;
markUsed(_i - _skipFirstArgs);
return true;
}
bool ContextMerge::handle_S() {
if ((_i+1) < _argc) {
if (_argv[_i+1][0] == '+') {
_desiredStrand = FileRecordMergeMgr::SAME_STRAND_FORWARD;
} else if (_argv[_i+1][0] == '-') {
_desiredStrand = FileRecordMergeMgr::SAME_STRAND_REVERSE;
}
markUsed(_i - _skipFirstArgs);
_i++;
markUsed(_i - _skipFirstArgs);
return true;
}
_errorMsg = "\n***** ERROR: -S option must be followed by + or -. *****";
return false;
}