int main()
{
// FRAGMENT(example)
// The horizontal and vertical sequence (database and query).
seqan::CharString seqH = "The quick BROWN fox jumped again!";
seqan::CharString seqV = "thick BROWN boxes of brownies!";
// ^^^
// Create seed and print the seeed sequence.
seqan::Seed<seqan::Simple> seed(11, 7, 14, 10);
// Perform match extension.
seqan::Score<int, seqan::Simple> scoringScheme(1, -1, -1);
extendSeed(seed, seqH, seqV, seqan::EXTEND_BOTH, scoringScheme, 3,
seqan::UnGappedXDrop());
// Perform a banded alignment.
seqan::Align<seqan::CharString> align;
resize(rows(align), 2);
assignSource(row(align, 0), infix(seqH, beginPositionH(seed),
endPositionH(seed)));
assignSource(row(align, 1), infix(seqV, beginPositionV(seed),
endPositionV(seed)));
// TODO(holtgrew): Use seed diagonals as bands.
globalAlignment(align, scoringScheme);
std::cerr << "Resulting alignment\n" << align << "\n";
// FRAGMENT(footer)
return 0;
}
void SimpleTableDump::dumpHeader(std::string name, std::shared_ptr<AbstractTable> table) {
std::stringstream header;
std::vector<std::string> names, types;
std::vector<uint32_t> parts;
// Get names and types
for(size_t i=0; i < table->columnCount(); ++i) {
names.push_back(table->nameOfColumn(i));
types.push_back(data_type_to_string(table->typeOfColumn(i)));
}
// This calculation will break if the width of the value_id changes
// or someone forgets to simply update the width accordingly in the
// constructor of the table
for(size_t i=0; i < table->partitionCount(); ++i) {
parts.push_back(table->partitionWidth(i));
}
// Dump and join
header << std::accumulate(names.begin(), names.end(), std::string(), infix(" | ")) << "\n";
header << std::accumulate(types.begin(), types.end(), std::string(), infix(" | ")) << "\n";
std::vector<std::string> allParts;
for(size_t i=0; i < parts.size(); ++i) {
auto p = parts[i];
auto tmp = std::vector<std::string>(p, std::to_string(i) + "_R");
allParts.insert(allParts.end(), tmp.begin(), tmp.end());
}
header << std::accumulate(allParts.begin(), allParts.end(), std::string(), infix(" | ")) << "\n";
header << "===";
std::string fullPath = _baseDirectory + "/" + name + "/header.dat";
std::ofstream data (fullPath, std::ios::out | std::ios::binary);
data << header.str();
data.close();
}
void ProjectSplicedRoi::updateRanges(seqan::GffRecord const & record)
{
// Get group name (possibly comma separated list).
seqan::CharString groupNames;
for (unsigned i = 0; i < length(record.tagNames); ++i)
if (record.tagNames[i] == groupBy)
groupNames = record.tagValues[i];
if (empty(groupNames))
return; // Record has no group names.
// Parse out the group names.
unsigned beginPos = 0;
unsigned endPos = 0;
for (; endPos <= length(groupNames); ++endPos)
{
if (endPos == length(groupNames) && beginPos < endPos) // Ignore empty keys.
{
_updateRanges(record, infix(groupNames, beginPos, endPos));
}
else if (groupNames[endPos] == ',')
{
if (beginPos < endPos) // Ignore empty keys.
_updateRanges(record, infix(groupNames, beginPos, endPos));
beginPos = endPos + 1;
}
}
}
void infix(treeNode *root)
{
if(root)
{
infix(root->lTree);
printf("%d\t",root -> data);
infix(root ->rTree);
}
}
void infix(tree* root)
{
if(root)
{
infix(root->left);
printf("%d\t",root -> data);
infix(root ->right);
}
}
void infix(Pointer<T> pointer)
{
if(pointer)
{
if(! is_leaf(pointer)) std::cout << "(";
infix(pointer->left_);
std::cout << pointer->val_;
infix(pointer->right_);
if(! is_leaf(pointer)) std::cout << ")";
}
}
//fills contingency tables with online pattern matching and kmerToID- method (see above)
void countFinds (Contingency & allContigs, seqan::StringSet<seqan::DnaString> kmers, Transcriptome transcripts){
timeval online;
gettimeofday(&online, NULL);
double startOnline= (online.tv_sec *1000000) + online.tv_usec;
// Database are the mRNAs from Transcriptome;
// Define the Aho-Corasick pattern over the kmers
seqan::Pattern<seqan::StringSet<seqan::DnaString>, seqan::AhoCorasick> pattern(kmers);
// Search for the kmers database sequence by database sequence.
//search kmers in down-/upregulated genes
unsigned id;
std::cout <<"processing mRNAs"<<'\n';
for (unsigned i = 0; i < length(transcripts.mRNAset); i++){
//std::cout <<"processing mRNA number"<<'\t'<< i<<'\n';
seqan::Finder<seqan::DnaString> finder(transcripts.mRNAset[i]); // new finder for each seq
while(find(finder, pattern)){
//assign the hit to the correct kmer sequence by converting the pattern sequence into an ID
id= kmerToID(infix(finder));
if(transcripts.isReg[i]){
allContigs.idDN[id].push_back(i);
}
else {
allContigs.idNoDN[id].push_back(i);
}
}
}
gettimeofday(&online, NULL);
double endOnline= (online.tv_sec *1000000) + online.tv_usec;
std::cout << length(kmers) << " kmers checked in " << (endOnline-startOnline)/1000000 << " seconds with Aho-Corasick pattern matching" << '\n';
}
// Simulate single-end sequencing from a fragment.
void SequencingSimulator::simulateSingleEnd(TRead & seq, TQualities & quals, SequencingSimulationInfo & info,
TFragment const & frag,
MethylationLevels const * levels)
{
bool isForward;
if (seqOptions->strands == SequencingOptions::BOTH)
isForward = (pickRandomNumber(rng, seqan::Pdf<seqan::Uniform<int> >(0, 1)) == 1);
else
isForward = (seqOptions->strands == SequencingOptions::FORWARD);
if (!seqOptions->bsSeqOptions.bsSimEnabled)
{
_simulateSingleEnd(seq, quals, info, frag, isForward);
}
else
{
SEQAN_ASSERT(levels);
bool bsForward = isForward;
// Re-pick strandedness of the BS-treated fragment.
if (seqOptions->bsSeqOptions.bsProtocol != BSSeqOptions::DIRECTIONAL)
bsForward = (pickRandomNumber(methRng, seqan::Pdf<seqan::Uniform<int> >(0, 1)) == 1);
_simulateBSTreatment(methFrag, frag, *levels, !bsForward);
_simulateSingleEnd(seq, quals, info, infix(methFrag, 0, length(methFrag)), isForward);
}
}
std::string* allt(int* idel, std::string ideligen) {
if (*idel > 3 || ideligen == "ifall")
return new std::string("igen");
int identifiering = *idel + 1;
std::string igenom("ihopkoppling");
int ihop = aning(&identifiering, igenom);
std::string* ikapp = new std::string("ilning");
int* illa = ann(identifiering, ikapp);
std::string* ilska = new std::string("implementering");
int* imperfekt = advent(identifiering, ilska);
std::string* inalles = new std::string("inblick");
int* inblandning = aftonsol(identifiering, inalles);
std::string* inbromsning = new std::string("indelning");
std::string indatagenerering = alltigenom(identifiering, inbromsning);
std::string indentering("indikering");
int indexering = aldrig(&identifiering, indentering);
std::string infix("informationsbit");
std::string* inflygning = alm(&identifiering, infix);
std::string ing("ingendera");
int ingalunda = andel(&identifiering, ing);
std::string* ingenstans = new std::string("ingetdera");
int* ingenting = allmoge(identifiering, ingenstans);
std::string* ingnidning = new std::string("initialisering");
return ingnidning;
} // allt
seqan::String<int> computeScore(TText const & text, TPattern const & pattern)
{
seqan::String<int> score;
seqan::resize(score, seqan::length(text), 0);
for (unsigned i = 0; i < seqan::length(text) - seqan::length(pattern) + 1; ++i)
score[i] = computeLocalScore(infix(text, i, i + seqan::length(pattern)), pattern);
return score;
}
int main(){
Integer ans;
char arr[128];
scanf("%[^\n]", arr); /* expression */
ans = infix(arr);
printf("Answer: ");
PrintInteger(ans);
return 0;
}
void main()
{
clrscr();
printf("\n Enter PostFix Expression :");
flushall();
gets(expr);
strcpy(str,infix());
printf("\n %s",str);
getch();
}
struct expr *infix(struct expr *left, char *expect)
{
exprlist_t args;
int toktype = tok->type;
char *ident;
switch (toktype)
{
case PLUS: case MINUS: case STAR: case SLASH: case OR: case XOR:
case LT: case LE: case GT: case GE: case NEQ: case EQ: case AND:
return binopexpr(left, toktype, expression(lbp(toktype)));
case LPAREN:
if (left->exprtype != identtype)
syntaxerror("calling non-callable expression");
args = empty_exprlist();
if (lookahead[0]->type != COMMA && lookahead[0]->type != RPAREN)
list_push_back(args, expression(0));
while (lookahead[0]->type == COMMA)
{
eat(COMMA);
list_push_back(args, expression(0));
}
eat(RPAREN);
ident = strdup(left->val.ident);
left->type = NULL; // To prevent segfaults when freeing the expr
free_expression(left);
return funcallexpr(ident, args);
case LSQBRACKET:
args = empty_exprlist();
list_push_back(args, expression(0));
while (lookahead[0]->type == COMMA)
{
eat(COMMA);
list_push_back(args, expression(0));
}
eat(RSQBRACKET);
return arrayexpr(left, args);
case DOT:
eat(IDENTIFIER);
char *ident = strdup(tok->val);
return record_access(left, ident);
case DEREF:
return make_deref(left);
default:
syntaxerror("expected %s, not %s", expect, tok->val);
next();
switch (tok->type)
{
case ENDOFFILE: return expr_from_val(0);
default: return infix(left, "expression");
}
}
}
struct expr *expression(int rbp)
{
next();
struct expr *left = prefix("expression");
struct pos pos;
left->pos = *tok->pos;
while (rbp < lbp(lookahead[0]->type))
{
next();
pos = left->pos;
left = infix(left, "expression");
left->pos.line = pos.line;
left->pos.charstart = pos.charstart;
left->pos.len = tok->pos->charstart + tok->pos->len - pos.charstart;
}
return left;
}
/*
* debug function, used only for view query
* which will be executed in non-leaf pages in index
*/
Datum
tsquerytree(PG_FUNCTION_ARGS)
{
QUERYTYPE *query = (QUERYTYPE *) DatumGetPointer(PG_DETOAST_DATUM(PG_GETARG_DATUM(0)));
INFIX nrm;
text *res;
ITEM *q;
int4 len;
if (query->size == 0)
{
res = (text *) palloc(VARHDRSZ);
VARATT_SIZEP(res) = VARHDRSZ;
PG_RETURN_POINTER(res);
}
q = clean_NOT_v2(GETQUERY(query), &len);
if (!q)
{
res = (text *) palloc(1 + VARHDRSZ);
VARATT_SIZEP(res) = 1 + VARHDRSZ;
*((char *) VARDATA(res)) = 'T';
}
else
{
nrm.curpol = q;
nrm.buflen = 32;
nrm.cur = nrm.buf = (char *) palloc(sizeof(char) * nrm.buflen);
*(nrm.cur) = '\0';
nrm.op = GETOPERAND(query);
infix(&nrm, true);
res = (text *) palloc(nrm.cur - nrm.buf + VARHDRSZ);
VARATT_SIZEP(res) = nrm.cur - nrm.buf + VARHDRSZ;
strncpy(VARDATA(res), nrm.buf, nrm.cur - nrm.buf);
pfree(q);
}
PG_FREE_IF_COPY(query, 0);
PG_RETURN_POINTER(res);
}
int main()
{
int totalNodesInTree , inFixArr[20] , preFixArr[20] ;
tree *root = NULL;
tree* pred = NULL;
int sum;
printf("\nEnter length of arr : ");
scanf("%d",&totalNodesInTree);
printf("\nEnter values of nodes in preorder\n");
scanArr(preFixArr,totalNodesInTree);
printArr(preFixArr,totalNodesInTree);
printf("\nEnter values of nodes in inorder\n");
scanArr(inFixArr,totalNodesInTree);
printArr(inFixArr,totalNodesInTree);
printf("\n\nPost Fix Order as shown :\n");
root = toPostFix(inFixArr,preFixArr,0,totalNodesInTree-1,0);
printf("\n");
printf("after creating tree :- \n");
printf("\nPrefix Notation\n");
prefix(root);
printf("\nInfix Notation\n");
infix(root);
printf("\nPostfix Notation\n");
postfix(root);
printf("\n");
if(isBst(root, &pred)){
printf("Its BST \n");
}
else{
printf("Its not BST\n");
}
printf("Final root pred => %d\n",pred -> data);
return 0;
}
int main()
{
int totalNodesInTree, inFixArr[15],preFixArr[15],nodeToBeDeleted;
treeNode *root = NULL;
printf("\nEnter length of arr : ");
scanf("%d",&totalNodesInTree);
printf("\nEnter values of nodes in preorder\n");
scanArr(preFixArr,totalNodesInTree);
printArr(preFixArr,totalNodesInTree);
printf("\nEnter values of nodes in inorder\n");
scanArr(inFixArr,totalNodesInTree);
printArr(inFixArr,totalNodesInTree);
printf("\n\nPost Fix Order as shown :\n");
root = toPostFix(inFixArr,preFixArr,0,totalNodesInTree-1,0);
printf("\n");
printf("after creating tree :- \n");
printf("\nPrefix Notation\n");
prefix(root);
printf("\nInfix Notation\n");
infix(root);
printf("\nPostfix Notation\n");
postfix(root);
printf("\n");
/* printf("Enter node to be deleted :- ");
scanf("%d",&nodeToBeDeleted);
root = deleteFromBst(root,nodeToBeDeleted);
*/
ClearTree(&root);
printf("After dispose :%d\n",root->data);
postfix(root);
printf("\n");
return 0;
}
Datum
bqarr_out(PG_FUNCTION_ARGS)
{
QUERYTYPE *query = (QUERYTYPE *) PG_DETOAST_DATUM(PG_GETARG_POINTER(0));
INFIX nrm;
if (query->size == 0)
ereport(ERROR,
(errcode(ERRCODE_INVALID_PARAMETER_VALUE),
errmsg("empty query")));
nrm.curpol = GETQUERY(query) + query->size - 1;
nrm.buflen = 32;
nrm.cur = nrm.buf = (char *) palloc(sizeof(char) * nrm.buflen);
*(nrm.cur) = '\0';
infix(&nrm, true);
PG_FREE_IF_COPY(query, 0);
PG_RETURN_POINTER(nrm.buf);
}
Datum
querytree(PG_FUNCTION_ARGS)
{
QUERYTYPE *query = (QUERYTYPE *) PG_GETARG_QUERYTYPE_P_COPY(0);
INFIX nrm;
text *res;
ITEM *q;
int4 len;
if (query->size == 0)
ereport(ERROR,
(errcode(ERRCODE_INVALID_PARAMETER_VALUE),
errmsg("empty query")));
q = (ITEM *) palloc(sizeof(ITEM) * query->size);
memcpy((void *) q, GETQUERY(query), sizeof(ITEM) * query->size);
len = shorterquery(q, query->size);
PG_FREE_IF_COPY(query, 0);
if (len == 0)
{
res = (text *) palloc(1 + VARHDRSZ);
SET_VARSIZE(res, 1 + VARHDRSZ);
*((char *) VARDATA(res)) = 'T';
}
else
{
nrm.curpol = q + len - 1;
nrm.buflen = 32;
nrm.cur = nrm.buf = (char *) palloc(sizeof(char) * nrm.buflen);
*(nrm.cur) = '\0';
infix(&nrm, true);
res = (text *) palloc(nrm.cur - nrm.buf + VARHDRSZ);
SET_VARSIZE(res, nrm.cur - nrm.buf + VARHDRSZ);
memcpy(VARDATA(res), nrm.buf, nrm.cur - nrm.buf);
}
pfree(q);
PG_RETURN_POINTER(res);
}
int main()
{
int hight,totalNodesInTree, inFixArr[15],preFixArr[15],nodeToBeDeleted;
treeNode *root = NULL;
printf("\nEnter length of arr : ");
scanf("%d",&totalNodesInTree);
printf("\nEnter values of nodes in preorder\n");
scanArr(preFixArr,totalNodesInTree);
printArr(preFixArr,totalNodesInTree);
printf("\nEnter values of nodes in inorder\n");
scanArr(inFixArr,totalNodesInTree);
printArr(inFixArr,totalNodesInTree);
printf("\n\nPost Fix Order as shown :\n");
root = toPostFix(inFixArr,preFixArr,0,totalNodesInTree-1,0);
printf("\n");
printf("after creating tree :- \n");
printf("\nPrefix Notation\n");
prefix(root);
printf("\nInfix Notation\n");
infix(root);
printf("\nPostfix Notation\n");
postfix(root);
printf("\n");
// printf("Enter node to be deleted :- ");
//scanf("%d",&nodeToBeDeleted);
//root = deleteFromBst(root,nodeToBeDeleted);
hight = hightOfBtree(root);
printf("Hight of Tree is :- %d\n",hight);
return 0;
}
void LLVM_Generator::visit (ast::Function_Declaration::Ptr node) {
auto& declarator = node->function_declarator();
// step 1
apply_indent_();
out_ << "declare ";
// step 2: function return type
out_ << type(node->type());
// step 3: function name
out_ << " @" << declarator->name();
// step 4: function argument list
out_ << "(";
infix(out_, ", ", declarator->argument_list(),
[] (parser::Symbol::Ptr symbol) { return type(symbol->type()); });
out_ << ")";
// step 5
out_ << std::endl;
}
Datum
ltxtq_out(PG_FUNCTION_ARGS)
{
ltxtquery *query = PG_GETARG_LTXTQUERY(0);
INFIX nrm;
if (query->size == 0)
ereport(ERROR,
(errcode(ERRCODE_SYNTAX_ERROR),
errmsg("syntax error"),
errdetail("Empty query.")));
nrm.curpol = GETQUERY(query);
nrm.buflen = 32;
nrm.cur = nrm.buf = (char *) palloc(sizeof(char) * nrm.buflen);
*(nrm.cur) = '\0';
nrm.op = GETOPERAND(query);
infix(&nrm, true);
PG_FREE_IF_COPY(query, 0);
PG_RETURN_POINTER(nrm.buf);
}
void LLVM_Generator::visit (ast::Function_Call::Ptr node) {
std::string register_ref = "%tmp." + to_string(register_reference_.size());
register_reference_[node] = register_ref;
auto& function = node->function();
auto& arguments = node->argument_list();
// Step 1: Prepare arguments
for (auto& argument : node->argument_list()) {
argument->emit_code(*this);
}
// // Step 2: call the function
// apply_indent_();
// out_ << register_ref << " = call " << type(function->type()) << " (";
// infix(out_, ", ", function->argument_list(),
// [] (parser::Symbol::Ptr symbol) { return type(symbol->type()); });
// out_ << ")* @" << function->name() << "(";
// infix(out_, ", ", arguments,
// [&] (ast::Expression::Ptr expr) {
// std::string tmp = type(expr->type()) + " " + register_reference_[expr];
// return tmp;// register_reference_[expr];
// });
// Step 2: call the function
apply_indent_();
out_ << register_ref << " = call " << type(function->type());
out_ << " @" << function->name() << "(";
infix(out_, ", ", arguments,
[&] (ast::Expression::Ptr expr) {
std::string tmp = type(expr->type()) + " " + register_reference_[expr];
return tmp;// register_reference_[expr];
});
out_ << ')' << std::endl;
}
Datum
tsquery_out(PG_FUNCTION_ARGS)
{
QUERYTYPE *query = (QUERYTYPE *) DatumGetPointer(PG_DETOAST_DATUM(PG_GETARG_DATUM(0)));
INFIX nrm;
if (query->size == 0)
{
char *b = palloc(1);
*b = '\0';
PG_RETURN_POINTER(b);
}
nrm.curpol = GETQUERY(query);
nrm.buflen = 32;
nrm.cur = nrm.buf = (char *) palloc(sizeof(char) * nrm.buflen);
*(nrm.cur) = '\0';
nrm.op = GETOPERAND(query);
infix(&nrm, true);
PG_FREE_IF_COPY(query, 0);
PG_RETURN_POINTER(nrm.buf);
}
Datum
querytree(PG_FUNCTION_ARGS)
{
QUERYTYPE *query = (QUERYTYPE *) PG_DETOAST_DATUM(PG_GETARG_POINTER(0));
INFIX nrm;
text *res;
ITEM *q;
int4 len;
if (query->size == 0)
ereport(ERROR,
(errcode(ERRCODE_INVALID_PARAMETER_VALUE),
errmsg("empty query")));
q = (ITEM *) palloc(sizeof(ITEM) * query->size);
memcpy((void *) q, GETQUERY(query), sizeof(ITEM) * query->size);
len = shorterquery(q, query->size);
PG_FREE_IF_COPY(query, 0);
if (len == 0)
{
res = cstring_to_text("T");
}
else
{
nrm.curpol = q + len - 1;
nrm.buflen = 32;
nrm.cur = nrm.buf = (char *) palloc(sizeof(char) * nrm.buflen);
*(nrm.cur) = '\0';
infix(&nrm, true);
res = cstring_to_text_with_len(nrm.buf, nrm.cur - nrm.buf);
}
pfree(q);
PG_RETURN_TEXT_P(res);
}
int main(int argc, char ** argv)
{
double startTime = 0;
// Parse command line.
SakOptions options;
seqan::ArgumentParser::ParseResult res = parseArgs(options, argc, argv);
if (res != seqan::ArgumentParser::PARSE_OK)
return res == seqan::ArgumentParser::PARSE_ERROR; // 1 on errors, 0 otherwise
// -----------------------------------------------------------------------
// Show options.
// -----------------------------------------------------------------------
if (options.verbosity >= 2)
{
std::cerr << "____OPTIONS___________________________________________________________________\n"
<< "\n"
<< "VERBOSITY " << options.verbosity << "\n"
<< "IN " << options.inFastxPath << "\n"
<< "OUT " << options.outPath << "\n"
<< "INFIX BEGIN " << options.seqInfixBegin << "\n"
<< "INFIX END " << options.seqInfixEnd << "\n"
<< "MAX LEN " << options.maxLength << "\n"
<< "READ PATTERN " << options.readPattern << "\n"
<< "REVCOMP " << yesNo(options.reverseComplement) << "\n"
<< "SEQUENCES\n";
for (unsigned i = 0; i < length(options.seqIndices); ++i)
std::cerr << " SEQ " << options.seqIndices[i] << "\n";
for (unsigned i = 0; i < length(options.seqIndexRanges); ++i)
std::cerr << " SEQS " << options.seqIndexRanges[i].i1 << "-" << options.seqIndexRanges[i].i2 << "\n";
}
// -----------------------------------------------------------------------
// Open Files.
// -----------------------------------------------------------------------
seqan::SeqFileIn inFile;
seqan::SeqFileOut outFile;
bool openRes = false;
if (!empty(options.inFastxPath))
openRes = open(inFile, toCString(options.inFastxPath));
else
openRes = open(inFile, std::cin);
if (!openRes)
{
std::cerr << "ERROR: Problem opening input file.\n";
return 1;
}
if (!empty(options.outPath))
openRes = open(outFile, toCString(options.outPath));
else
openRes = open(outFile, std::cout, seqan::Fastq());
if (!openRes)
{
std::cerr << "ERROR: Problem opening output file.\n";
return 1;
}
// Compute index of last sequence to write if any.
uint64_t endIdx = seqan::maxValue<uint64_t>();
for (unsigned i = 0; i < length(options.seqIndices); ++i)
if (endIdx == seqan::maxValue<uint64_t>() || endIdx > options.seqIndices[i] + 1)
endIdx = options.seqIndices[i] + 1;
for (unsigned i = 0; i < length(options.seqIndexRanges); ++i)
if (endIdx == seqan::maxValue<uint64_t>() || endIdx > options.seqIndexRanges[i].i2)
endIdx = options.seqIndexRanges[i].i2;
if (options.verbosity >= 2)
std::cerr << "Sequence end idx: " << endIdx << "\n";
// -----------------------------------------------------------------------
// Read and Write Filtered.
// -----------------------------------------------------------------------
startTime = seqan::sysTime();
unsigned idx = 0;
uint64_t charsWritten = 0;
seqan::CharString id;
seqan::CharString seq;
seqan::CharString quals;
while (!atEnd(inFile) && charsWritten < options.maxLength && idx < endIdx)
{
try
{
readRecord(id, seq, quals, inFile);
}
catch (seqan::ParseError const & e)
{
std::cerr << "ERROR: Problem reading file: " << e.what() << "\n";
return 1;
}
// Check whether to write out sequence.
bool writeOut = false;
if (empty(options.seqIndices) && empty(options.seqIndexRanges))
writeOut = true;
// One of options.seqIndices.
if (!writeOut)
{
for (unsigned i = 0; i < length(options.seqIndices); ++i)
{
if (options.seqIndices[i] == idx)
{
writeOut = true;
break;
}
}
}
// One of options.seqIndexRanges.
if (!writeOut)
{
for (unsigned i = 0; i < length(options.seqIndexRanges); ++i)
{
if (idx >= options.seqIndexRanges[i].i1 && idx < options.seqIndexRanges[i].i2)
{
writeOut = true;
break;
}
}
}
// Name pattern matches.
if (!writeOut && !empty(options.readPattern))
{
unsigned l = length(options.readPattern);
if (l > length(id))
l = length(id);
if (prefix(id, l) == prefix(options.readPattern, l))
writeOut = true;
}
// Write out if we want this.
if (writeOut)
{
// Get begin and end index of infix to write out.
uint64_t infixBegin = 0;
if (options.seqInfixBegin != seqan::maxValue<uint64_t>())
infixBegin = options.seqInfixBegin;
if (infixBegin > length(seq))
infixBegin = length(seq);
uint64_t infixEnd = length(seq);
if (options.seqInfixEnd < length(seq))
infixEnd = options.seqInfixEnd;
if (infixEnd < infixBegin)
infixEnd = infixBegin;
if (options.verbosity >= 3)
std::cerr << "INFIX\tbegin:" << infixBegin << "\tend:" << infixEnd << "\n";
if (options.reverseComplement)
{
seqan::Dna5String seqCopy = seq;
reverseComplement(seqCopy);
reverse(quals);
infixEnd = length(seq) - infixEnd;
infixBegin = length(seq) - infixBegin;
std::swap(infixEnd, infixBegin);
writeRecord(outFile, id, infix(seqCopy, infixBegin, infixEnd), infix(quals, infixBegin, infixEnd));
}
else
writeRecord(outFile, id, infix(seq, infixBegin, infixEnd), infix(quals, infixBegin, infixEnd));
}
// Advance counter idx.
idx += 1;
}
if (options.verbosity >= 2)
std::cerr << "Took " << (seqan::sysTime() - startTime) << " s\n";
return 0;
}
static void
infix(INFIX *in, bool first)
{
if (in->curpol->type == VAL)
{
RESIZEBUF(in, 11);
sprintf(in->cur, "%d", in->curpol->val);
in->cur = strchr(in->cur, '\0');
in->curpol--;
}
else if (in->curpol->val == (int4) '!')
{
bool isopr = false;
RESIZEBUF(in, 1);
*(in->cur) = '!';
in->cur++;
*(in->cur) = '\0';
in->curpol--;
if (in->curpol->type == OPR)
{
isopr = true;
RESIZEBUF(in, 2);
sprintf(in->cur, "( ");
in->cur = strchr(in->cur, '\0');
}
infix(in, isopr);
if (isopr)
{
RESIZEBUF(in, 2);
sprintf(in->cur, " )");
in->cur = strchr(in->cur, '\0');
}
}
else
{
int4 op = in->curpol->val;
INFIX nrm;
in->curpol--;
if (op == (int4) '|' && !first)
{
RESIZEBUF(in, 2);
sprintf(in->cur, "( ");
in->cur = strchr(in->cur, '\0');
}
nrm.curpol = in->curpol;
nrm.buflen = 16;
nrm.cur = nrm.buf = (char *) palloc(sizeof(char) * nrm.buflen);
/* get right operand */
infix(&nrm, false);
/* get & print left operand */
in->curpol = nrm.curpol;
infix(in, false);
/* print operator & right operand */
RESIZEBUF(in, 3 + (nrm.cur - nrm.buf));
sprintf(in->cur, " %c %s", op, nrm.buf);
in->cur = strchr(in->cur, '\0');
pfree(nrm.buf);
if (op == (int4) '|' && !first)
{
RESIZEBUF(in, 2);
sprintf(in->cur, " )");
in->cur = strchr(in->cur, '\0');
}
}
}
void infix_print() const { infix(root_); }
namespace cat
{
//////////////////////////////////////////////////////////////////////////////////
//
// identity function
//
struct Identity
{
using function_type = placeholders::_a(placeholders::_a);
template <typename T>
constexpr auto
operator()(T &&x) const noexcept
{
return std::forward<T>(x);
}
};
constexpr Identity identity = {};
//////////////////////////////////////////////////////////////////////////////////
//
// make_function
//
template<typename F>
auto constexpr make_function(F &&f)
{
return std::function<typename function_type<F>::type>(std::forward<F>(f));
}
//////////////////////////////////////////////////////////////////////////////////
//
// first, second, elem<> on pair/tuple...:
//
struct First_
{
using function_type = placeholders::_a(std::pair<placeholders::_a, placeholders::_b>);
template <typename P>
constexpr decltype(auto)
operator()(P && p) const noexcept
{
return std::get<0>(std::forward<P>(p));
}
} constexpr first = First_{};
struct Second_
{
using function_type = placeholders::_b(std::pair<placeholders::_a, placeholders::_b>);
template <typename P>
constexpr decltype(auto)
operator()(P &&p) const noexcept
{
return std::get<1>(std::forward<P>(p));
}
} constexpr second = Second_{};
template <size_t N>
struct Elem_
{
using function_type = placeholders::unspec(std::tuple<placeholders::unspec>);
template <typename Tuple>
constexpr decltype(auto)
operator()(Tuple && t) const noexcept
{
return std::get<N>(std::forward<Tuple>(t));
}
};
#if defined(__clang__)
template <size_t N>
constexpr auto elem = Elem_<N>{};
#endif
//////////////////////////////////////////////////////////////////////////////////
//
// Callable_ with partial application support
//
namespace details
{
//
// Argument decay on the basis of the target signature.
//
template <typename F, size_t Idx, typename T>
struct currying_decay
{
using Tp = arg_type_at_t<Idx, F>;
using type = typename std::conditional<
std::is_lvalue_reference<Tp>::value,
T, std::decay_t<T> >::type;
};
template <typename F, size_t Idx, typename T>
using currying_decay_t = typename currying_decay<F, Idx, T>::type;
}
template <typename F, typename ...Ts>
struct Callable_
{
using function_type =
typename meta::partial_function_type<
typename function_type<F>::type, sizeof...(Ts)>::type;
template <typename ...Xs>
constexpr explicit Callable_(F fun, std::tuple<Xs...> args = std::tuple<Xs...>{})
: fun_(std::move(fun))
, args_(std::move(args))
{ }
template <typename ...Xs>
auto operator()(Xs && ... xs) const
{
constexpr size_t N = function_arity<F>::value - sizeof...(Ts);
static_assert(N >= sizeof...(Xs), "Too many argument!");
return eval_(std::integral_constant<size_t, N - sizeof...(Xs)>(), std::make_index_sequence<sizeof...(Xs)>(), std::forward<Xs>(xs)...);
}
template <typename ...Xs>
auto apply(Xs && ... xs) const
{
constexpr size_t N = function_arity<F>::value - sizeof...(Ts);
static_assert(N >= sizeof...(Xs), "Too many argument!");
return apply_(std::integral_constant<size_t, N - sizeof...(Xs)>(), std::make_index_sequence<sizeof...(Xs)>(), std::forward<Xs>(xs)...);
}
private:
template <size_t ...N, typename ...Xs>
auto eval_(std::integral_constant<size_t, 0>, std::index_sequence<N...>, Xs &&...xs) const
{
return tuple_apply(fun_, std::tuple_cat(args_, std::forward_as_tuple(std::forward<Xs>(xs)...)));
}
template <size_t I, size_t ...N, typename ...Xs>
auto eval_(std::integral_constant<size_t, I>, std::index_sequence<N...>, Xs &&...xs) const
{
return Callable_<F, Ts..., details::currying_decay_t<function_type, N, Xs>...>(
fun_, std::tuple_cat(args_, std::forward_as_tuple(std::forward<Xs>(xs)...)));
}
template <size_t I, size_t ...N, typename ...Xs>
auto apply_(std::integral_constant<size_t, I>, std::index_sequence<N...>, Xs &&...xs) const
{
return Callable_<F, Ts..., details::currying_decay_t<function_type, N, Xs>...>(
fun_, std::tuple_cat(args_, std::forward_as_tuple(std::forward<Xs>(xs)...)));
}
F fun_;
std::tuple<Ts...> args_;
};
template<typename F>
constexpr auto curry(F && f)
{
return Callable_<std::decay_t<F>>(std::forward<F>(f));
}
template<typename F, typename ...Ts>
constexpr auto curry(F && f, Ts&& ...xs)
{
return curry(std::forward<F>(f)).apply(std::forward<Ts>(xs)...);
}
//////////////////////////////////////////////////////////////////////////////////
//
// Generic callable (for generic lambdas and polymorphic C++ callable objects)
//
template <typename Fun, typename F>
struct Callable_as_
{
using function_type = Fun;
constexpr Callable_as_()
: fun_{}
{ }
constexpr Callable_as_(F f)
: fun_(std::move(f))
{ }
template <typename ...Ts>
constexpr decltype(auto)
operator()(Ts&& ... xs) const
{
return fun_(std::forward<Ts>(xs)...);
}
F fun_;
};
template <typename Fun, typename F>
constexpr auto curry_as(F && f)
{
return curry(Callable_as_<Fun, std::decay_t<F>>(std::forward<F>(f)));
};
template <typename Fun, typename F, typename ...Ts>
constexpr auto curry_as(F && f, Ts && ... xs)
{
return curry_as<Fun>(std::forward<F>(f)).apply(std::forward<Ts>(xs)...);
};
//////////////////////////////////////////////////////////////////////////////////
//
// Compose_: functional composition of callable types
//
template <typename F, typename G, typename = void> struct Compose_;
template <typename F, typename G>
struct Compose_<F, G, std::enable_if_t<function_arity<G>::value != 0>>
{
using function_type = meta::compose_function_type_t<
function_type_t<F>,
function_type_t<G>>;
constexpr Compose_(F f, G g)
: f_(std::move(f))
, g_(std::move(g))
{ }
template <typename T, typename ...Ts>
constexpr decltype(auto)
operator()(T &&x, Ts && ...xs) const
{
return f_( g_(std::forward<T>(x)), std::forward<Ts>(xs)...);
}
F f_;
G g_;
};
template <typename F, typename G>
struct Compose_<F, G, std::enable_if_t<function_arity<G>::value == 0>>
{
using function_type = meta::compose_function_type_t<
function_type_t<F>,
function_type_t<G>>;
constexpr Compose_(F f, G g)
: f_(std::move(f))
, g_(std::move(g))
{ }
template <typename ...Ts>
constexpr decltype(auto)
operator()(Ts && ...xs) const
{
return f_( g_(), std::forward<Ts>(xs)...);
}
F f_;
G g_;
};
template <typename F, typename G>
constexpr auto compose(F && f, G && g)
{
static_assert(is_callable<F>::value && is_callable<G>::value,
"compose: F and G must be callable types");
return Compose_<std::decay_t<F>,std::decay_t<G>>{ std::forward<F>(f), std::forward<G>(g) };
}
template <typename F, typename G,
std::enable_if_t<is_callable<F>::value && is_callable<G>::value> * = nullptr>
constexpr auto operator^(F && f, G && g)
{
return compose(std::forward<F>(f), std::forward<G>(g));
}
//////////////////////////////////////////////////////////////////////////////////
//
// flip:
//
template <typename F>
struct Flip_
{
using function_type = meta::flip_function_type_t<function_type_t<F>>;
constexpr Flip_(F fun)
: fun_(std::move(fun))
{ }
template <typename T1, typename T2, typename ...Ts>
constexpr decltype(auto)
operator()(T1 && x1, T2 && x2, Ts && ...xs) const
{
return fun_(std::forward<T2>(x2),
std::forward<T1>(x1),
std::forward<Ts>(xs)...);
}
private:
F fun_;
};
template <typename F>
constexpr auto flip(F && fun_)
{
return Flip_<std::decay_t<F>>{ std::forward<F>(fun_) };
};
//////////////////////////////////////////////////////////////////////////////////
//
// on (infix version):
//
template <typename F, typename G>
struct On_
{
using function_type = meta::on_function_type_t<function_type_t<F>,
function_type_t<G>>;
constexpr On_(F f, G g)
: f_(std::move(f))
, g_(std::move(g))
{ }
template <typename T1, typename T2, typename ...Ts>
constexpr decltype(auto)
operator()(T1 && x1, T2 && x2, Ts && ...xs) const
{
return f_(g_(std::forward<T1>(x1)),
g_(std::forward<T2>(x2)), std::forward<Ts>(xs)...);
}
private:
F f_;
G g_;
};
struct on_
{
template <typename F, typename G>
constexpr auto
operator()(F f_, G g_) const
{
return On_<F,G>{ std::move(f_), std::move(g_) };
};
};
constexpr auto on = infix(on_{});
//////////////////////////////////////////////////////////////////////////////////
//
// constant
//
template <typename T>
struct Constant_
{
using function_type = T(placeholders::unspec);
template <typename Tp>
constexpr T operator()(Tp const &) const
{
return value_;
}
T value_;
};
template <typename T>
constexpr auto constant(T && value)
{
return Constant_<std::decay_t<T>>{ std::forward<T>(value) };
}
} // namespace cat
/*
* recursive walk on tree and print it in
* infix (human-readable) view
*/
static void
infix(INFIX * in, bool first)
{
if (in->curpol->type == VAL)
{
char *op = in->op + in->curpol->distance;
RESIZEBUF(in, in->curpol->length * 2 + 2 + 5);
*(in->cur) = '\'';
in->cur++;
while (*op)
{
if (*op == '\'')
{
*(in->cur) = '\\';
in->cur++;
}
*(in->cur) = *op;
op++;
in->cur++;
}
*(in->cur) = '\'';
in->cur++;
if (in->curpol->weight)
{
*(in->cur) = ':';
in->cur++;
if (in->curpol->weight & (1 << 3))
{
*(in->cur) = 'A';
in->cur++;
}
if (in->curpol->weight & (1 << 2))
{
*(in->cur) = 'B';
in->cur++;
}
if (in->curpol->weight & (1 << 1))
{
*(in->cur) = 'C';
in->cur++;
}
if (in->curpol->weight & 1)
{
*(in->cur) = 'D';
in->cur++;
}
}
*(in->cur) = '\0';
in->curpol++;
}
else if (in->curpol->val == (int4) '!')
{
bool isopr = false;
RESIZEBUF(in, 1);
*(in->cur) = '!';
in->cur++;
*(in->cur) = '\0';
in->curpol++;
if (in->curpol->type == OPR)
{
isopr = true;
RESIZEBUF(in, 2);
sprintf(in->cur, "( ");
in->cur = strchr(in->cur, '\0');
}
infix(in, isopr);
if (isopr)
{
RESIZEBUF(in, 2);
sprintf(in->cur, " )");
in->cur = strchr(in->cur, '\0');
}
}
else
{
int4 op = in->curpol->val;
INFIX nrm;
in->curpol++;
if (op == (int4) '|' && !first)
{
RESIZEBUF(in, 2);
sprintf(in->cur, "( ");
in->cur = strchr(in->cur, '\0');
}
nrm.curpol = in->curpol;
nrm.op = in->op;
nrm.buflen = 16;
nrm.cur = nrm.buf = (char *) palloc(sizeof(char) * nrm.buflen);
/* get right operand */
infix(&nrm, false);
/* get & print left operand */
in->curpol = nrm.curpol;
infix(in, false);
/* print operator & right operand */
RESIZEBUF(in, 3 + (nrm.cur - nrm.buf));
sprintf(in->cur, " %c %s", op, nrm.buf);
in->cur = strchr(in->cur, '\0');
pfree(nrm.buf);
if (op == (int4) '|' && !first)
{
RESIZEBUF(in, 2);
sprintf(in->cur, " )");
in->cur = strchr(in->cur, '\0');
}
}
}
