//
#include "command.hpp"
+#include "sequence.hpp"
+#include "qualityscores.h"
+#include "alignment.hpp"
+#include "gotohoverlap.hpp"
+#include "needlemanoverlap.hpp"
+#include "blastalign.hpp"
+#include "noalign.hpp"
+
struct fastqRead {
vector<int> scores;
fastqRead readFastq(ifstream&);
vector< vector<string> > readFastqFiles(int&);
bool checkReads(fastqRead&, fastqRead&);
+ int createProcesses(vector< vector<string> >, string, string, string);
+ int driver(vector<string>, string, string, string);
};
/**************************************************************************************************/
+/**************************************************************************************************/
+//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 contigsData {
+ string outputFasta;
+ string outputQual;
+ string outputMisMatches;
+ string align;
+ vector<string> files;
+ MothurOut* m;
+ float match, misMatch, gapOpen, gapExtend;
+ int count, threadID;
+
+ contigsData(){}
+ contigsData(vector<string> f, string of, string oq, string om, string al, MothurOut* mout, float ma, float misMa, float gapO, float gapE, int tid) {
+ files = f;
+ outputFasta = of;
+ outputQual = oq;
+ outputMisMatches = om;
+ m = mout;
+ match = ma;
+ misMatch = misMa;
+ gapOpen = gapO;
+ gapExtend = gapE;
+ align = al;
+ count = 0;
+ threadID = tid;
+ }
+};
-
-
-
+/**************************************************************************************************/
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+#else
+static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
+ contigsData* pDataArray;
+ pDataArray = (contigsData*)lpParam;
+
+ try {
+ int longestBase = 1000;
+ Alignment* alignment;
+ if(pDataArray->align == "gotoh") { alignment = new GotohOverlap(pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch, longestBase); }
+ else if(pDataArray->align == "needleman") { alignment = new NeedlemanOverlap(pDataArray->gapOpen, pDataArray->match, pDataArray->misMatch, longestBase); }
+
+ int num = 0;
+ string thisffastafile = pDataArray->files[0];
+ string thisfqualfile = pDataArray->files[1];
+ string thisrfastafile = pDataArray->files[2];
+ string thisrqualfile = pDataArray->files[3];
+
+ if (pDataArray->m->debug) { pDataArray->m->mothurOut("[DEBUG]: ffasta = " + thisffastafile + ".\n[DEBUG]: fqual = " + thisfqualfile + ".\n[DEBUG]: rfasta = " + thisrfastafile + ".\n[DEBUG]: rqual = " + thisrqualfile + ".\n"); }
+
+ ifstream inFFasta, inRFasta, inFQual, inRQual;
+ pDataArray->m->openInputFile(thisffastafile, inFFasta);
+ pDataArray->m->openInputFile(thisfqualfile, inFQual);
+ pDataArray->m->openInputFile(thisrfastafile, inRFasta);
+ pDataArray->m->openInputFile(thisrqualfile, inRQual);
+
+ ofstream outFasta, outQual, outMisMatch;
+ pDataArray->m->openOutputFile(pDataArray->outputFasta, outFasta);
+ pDataArray->m->openOutputFile(pDataArray->outputQual, outQual);
+ pDataArray->m->openOutputFile(pDataArray->outputMisMatches, outMisMatch);
+ outMisMatch << "Name\tLength\tMisMatches\n";
+
+ while ((!inFQual.eof()) && (!inFFasta.eof()) && (!inRFasta.eof()) && (!inRQual.eof())) {
+
+ if (pDataArray->m->control_pressed) { break; }
+
+ //read seqs and quality info
+ Sequence fSeq(inFFasta); pDataArray->m->gobble(inFFasta);
+ Sequence rSeq(inRFasta); pDataArray->m->gobble(inRFasta);
+ QualityScores fQual(inFQual); pDataArray->m->gobble(inFQual);
+ QualityScores rQual(inRQual); pDataArray->m->gobble(inRQual);
+
+ //flip the reverse reads
+ rSeq.reverseComplement();
+ rQual.flipQScores();
+
+ //pairwise align
+ alignment->align(fSeq.getUnaligned(), rSeq.getUnaligned());
+ map<int, int> ABaseMap = alignment->getSeqAAlnBaseMap();
+ map<int, int> BBaseMap = alignment->getSeqBAlnBaseMap();
+ fSeq.setAligned(alignment->getSeqAAln());
+ rSeq.setAligned(alignment->getSeqBAln());
+ int length = fSeq.getAligned().length();
+
+ //traverse alignments merging into one contiguous seq
+ string contig = "";
+ vector<int> contigScores;
+ int numMismatches = 0;
+ string seq1 = fSeq.getAligned();
+ string seq2 = rSeq.getAligned();
+
+ vector<int> scores1 = fQual.getQualityScores();
+ vector<int> scores2 = rQual.getQualityScores();
+
+ for (int i = 0; i < length; i++) {
+ if (seq1[i] == seq2[i]) { //match, add base and choose highest score
+ contig += seq1[i];
+ contigScores.push_back(scores1[ABaseMap[i]]);
+ if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { contigScores[i] = scores2[BBaseMap[i]]; }
+ }else if (((seq1[i] == '.') || (seq1[i] == '-')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //seq1 is a gap and seq2 is a base, choose seq2
+ contig += seq2[i];
+ contigScores.push_back(scores2[BBaseMap[i]]);
+ }else if (((seq2[i] == '.') || (seq2[i] == '-')) && ((seq1[i] != '-') && (seq1[i] != '.'))) { //seq2 is a gap and seq1 is a base, choose seq1
+ contig += seq1[i];
+ contigScores.push_back(scores1[ABaseMap[i]]);
+ }else if (((seq1[i] != '-') && (seq1[i] != '.')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //both bases choose one with better quality
+ char c = seq1[i];
+ contigScores.push_back(scores1[ABaseMap[i]]);
+ if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { contigScores[i] = scores2[BBaseMap[i]]; c = seq2[i]; }
+ contig += c;
+ numMismatches++;
+ }else { //should never get here
+ pDataArray->m->mothurOut("[ERROR]: case I didn't think of seq1 = " + toString(seq1[i]) + " and seq2 = " + toString(seq2[i]) + "\n");
+ }
+ }
+
+ //output
+ outFasta << ">" << fSeq.getName() << endl << contig << endl;
+ outQual << ">" << fSeq.getName() << endl;
+ for (int i = 0; i < contigScores.size(); i++) { outQual << contigScores[i] << ' '; }
+ outQual << endl;
+ outMisMatch << fSeq.getName() << '\t' << contig.length() << '\t' << numMismatches << endl;
+
+ num++;
+
+ //report progress
+ if((num) % 1000 == 0){ pDataArray->m->mothurOut(toString(num)); pDataArray->m->mothurOutEndLine(); }
+ }
+
+ //report progress
+ if((num) % 1000 != 0){ pDataArray->m->mothurOut(toString(num)); pDataArray->m->mothurOutEndLine(); }
+
+ inFFasta.close();
+ inFQual.close();
+ inRFasta.close();
+ inRQual.close();
+ outFasta.close();
+ outQual.close();
+ outMisMatch.close();
+ delete alignment;
+
+ if (pDataArray->m->control_pressed) { pDataArray->m->mothurRemove(pDataArray->outputQual); pDataArray->m->mothurRemove(pDataArray->outputFasta); pDataArray->m->mothurRemove(pDataArray->outputMisMatches);}
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ pDataArray->m->errorOut(e, "AlignCommand", "MyContigsThreadFunction");
+ exit(1);
+ }
+}
+#endif
#endif
projects / mothur.git / blobdiff