*/
#include "mothur.h"
#include "command.hpp"
+#include "sequence.hpp"
class ScreenSeqsCommand : public Command {
linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
};
- vector<int> processIDS; //processid
- vector<linePair*> lines;
+ vector<linePair> lines;
int screenNameGroupFile(set<string>);
int screenGroupFile(set<string>);
int screenQual(set<string>);
int screenTaxonomy(set<string>);
- int driver(linePair*, string, string, string, set<string>&);
+ int driver(linePair, string, string, string, set<string>&);
int createProcesses(string, string, string, set<string>&);
#ifdef USE_MPI
int getSummary(vector<unsigned long long>&);
int createProcessesCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string);
- int driverCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string, linePair*);
+ int driverCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string, linePair);
};
+/**************************************************************************************************/
+//custom data structure for threads to use.
+// This is passed by void pointer so it can be any data type
+// that can be passed using a single void pointer (LPVOID).
+struct sumData {
+ vector<int> startPosition;
+ vector<int> endPosition;
+ vector<int> seqLength;
+ vector<int> ambigBases;
+ vector<int> longHomoPolymer;
+ string filename, namefile;
+ unsigned long long start;
+ unsigned long long end;
+ int count;
+ MothurOut* m;
+ map<string, int> nameMap;
+
+
+ sumData(){}
+ sumData(string f, MothurOut* mout, unsigned long long st, unsigned long long en, string nf, map<string, int> nam) {
+ filename = f;
+ namefile = nf;
+ m = mout;
+ start = st;
+ end = en;
+ nameMap = nam;
+ count = 0;
+ }
+};
+/**************************************************************************************************/
+//custom data structure for threads to use.
+// This is passed by void pointer so it can be any data type
+// that can be passed using a single void pointer (LPVOID).
+struct sumScreenData {
+ int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength;
+ unsigned long long start;
+ unsigned long long end;
+ int count;
+ MothurOut* m;
+ string goodFName, badAccnosFName, filename;
+ set<string>* badSeqNames;
+
+
+ sumScreenData(){}
+ sumScreenData(int s, int e, int a, int h, int minl, int maxl, string f, MothurOut* mout, unsigned long long st, unsigned long long en, string gf, string bf, set<string>* bn) {
+ startPos = s;
+ endPos = e;
+ minLength = minl;
+ maxLength = maxl;
+ maxAmbig = a;
+ maxHomoP = h;
+ filename = f;
+ goodFName = gf;
+ badAccnosFName = bf;
+ m = mout;
+ start = st;
+ end = en;
+ badSeqNames = bn;
+ count = 0;
+ }
+};
+
+
+/**************************************************************************************************/
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#else
+static DWORD WINAPI MySumThreadFunction(LPVOID lpParam){
+ sumData* pDataArray;
+ pDataArray = (sumData*)lpParam;
+
+ try {
+ ifstream in;
+ pDataArray->m->openInputFile(pDataArray->filename, in);
+
+ //print header if you are process 0
+ if ((pDataArray->start == 0) || (pDataArray->start == 1)) {
+ in.seekg(0);
+ }else { //this accounts for the difference in line endings.
+ in.seekg(pDataArray->start-1); pDataArray->m->gobble(in);
+ }
+
+ pDataArray->count = pDataArray->end;
+ for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process
+
+ if (pDataArray->m->control_pressed) { in.close(); pDataArray->count = 1; return 1; }
+
+ Sequence current(in); pDataArray->m->gobble(in);
+
+ if (current.getName() != "") {
+
+ int num = 1;
+ if (pDataArray->namefile != "") {
+ //make sure this sequence is in the namefile, else error
+ map<string, int>::iterator it = pDataArray->nameMap.find(current.getName());
+
+ if (it == pDataArray->nameMap.end()) { pDataArray->m->mothurOut("[ERROR]: " + current.getName() + " is not in your namefile, please correct."); pDataArray->m->mothurOutEndLine(); pDataArray->m->control_pressed = true; }
+ else { num = it->second; }
+ }
+
+ //for each sequence this sequence represents
+ for (int i = 0; i < num; i++) {
+ pDataArray->startPosition.push_back(current.getStartPos());
+ pDataArray->endPosition.push_back(current.getEndPos());
+ pDataArray->seqLength.push_back(current.getNumBases());
+ pDataArray->ambigBases.push_back(current.getAmbigBases());
+ pDataArray->longHomoPolymer.push_back(current.getLongHomoPolymer());
+ }
+ }
+ }
+
+ in.close();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ pDataArray->m->errorOut(e, "ScreenSeqsCommand", "MySumThreadFunction");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+
+static DWORD WINAPI MySumScreenThreadFunction(LPVOID lpParam){
+ sumScreenData* pDataArray;
+ pDataArray = (sumScreenData*)lpParam;
+
+ try {
+
+ ofstream goodFile;
+ pDataArray->m->openOutputFile(pDataArray->goodFName, goodFile);
+
+ ofstream badAccnosFile;
+ pDataArray->m->openOutputFile(pDataArray->badAccnosFName, badAccnosFile);
+
+ ifstream in;
+ pDataArray->m->openInputFile(pDataArray->filename, in);
+
+ //print header if you are process 0
+ if ((pDataArray->start == 0) || (pDataArray->start == 1)) {
+ in.seekg(0);
+ }else { //this accounts for the difference in line endings.
+ in.seekg(pDataArray->start-1); pDataArray->m->gobble(in);
+ }
+
+ pDataArray->count = pDataArray->end;
+ for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process
+
+ if (pDataArray->m->control_pressed) { in.close(); badAccnosFile.close(); goodFile.close(); pDataArray->count = 1; return 1; }
+
+ Sequence currSeq(in); pDataArray->m->gobble(in);
+
+ if (currSeq.getName() != "") {
+ bool goodSeq = 1; // innocent until proven guilty
+ if(goodSeq == 1 && pDataArray->startPos != -1 && pDataArray->startPos < currSeq.getStartPos()) { goodSeq = 0; }
+ if(goodSeq == 1 && pDataArray->endPos != -1 && pDataArray->endPos > currSeq.getEndPos()) { goodSeq = 0; }
+ if(goodSeq == 1 && pDataArray->maxAmbig != -1 && pDataArray->maxAmbig < currSeq.getAmbigBases()) { goodSeq = 0; }
+ if(goodSeq == 1 && pDataArray->maxHomoP != -1 && pDataArray->maxHomoP < currSeq.getLongHomoPolymer()) { goodSeq = 0; }
+ if(goodSeq == 1 && pDataArray->minLength != -1 && pDataArray->minLength > currSeq.getNumBases()) { goodSeq = 0; }
+ if(goodSeq == 1 && pDataArray->maxLength != -1 && pDataArray->maxLength < currSeq.getNumBases()) { goodSeq = 0; }
+
+ if(goodSeq == 1){
+ currSeq.printSequence(goodFile);
+ }
+ else{
+ badAccnosFile << currSeq.getName() << endl;
+ pDataArray->badSeqNames->insert(currSeq.getName());
+ }
+
+ }
+ //report progress
+ if((i+1) % 100 == 0){ pDataArray->m->mothurOut("Processing sequence: " + toString(i+1)); pDataArray->m->mothurOutEndLine(); }
+ }
+ //report progress
+ if((pDataArray->count) % 100 != 0){ pDataArray->m->mothurOut("Processing sequence: " + toString(pDataArray->count)); pDataArray->m->mothurOutEndLine(); }
+
+
+
+ in.close();
+ goodFile.close();
+ badAccnosFile.close();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ pDataArray->m->errorOut(e, "ScreenSeqsCommand", "MySumScreenThreadFunction");
+ exit(1);
+ }
+}
+
+#endif
+
+/**************************************************************************************************/
+
+
+
#endif
projects / mothur.git / blobdiff