X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=trimseqscommand.h;h=14eed17e236a333583d461d61482a1d541c6a9cf;hp=80e1ebe1a00e2f56ec19a6f23c3ba890af1c4f10;hb=a2cde58c1e72199498a2142983ef040dce36da10;hpb=c85db0a4be3a1f8037a71a23ca73f9762184e28a diff --git a/trimseqscommand.h b/trimseqscommand.h index 80e1ebe..14eed17 100644 --- a/trimseqscommand.h +++ b/trimseqscommand.h @@ -55,12 +55,14 @@ private: bool abort, createGroup; string fastaFile, oligoFile, qFileName, groupfile, nameFile, countfile, outputDir; - bool flip, allFiles, qtrim, keepforward; + bool flip, allFiles, qtrim, keepforward, pairedOligos, reorient, logtransform; int numFPrimers, numRPrimers, numLinkers, numSpacers, maxAmbig, maxHomoP, minLength, maxLength, processors, tdiffs, bdiffs, pdiffs, ldiffs, sdiffs, comboStarts; int qWindowSize, qWindowStep, keepFirst, removeLast; double qRollAverage, qThreshold, qWindowAverage, qAverage; vector revPrimer, outputNames; set filesToRemove; + map pairedBarcodes; + map pairedPrimers; map barcodes; vector groupVector; map primers; @@ -96,7 +98,7 @@ struct trimData { vector > qualFileNames; vector > nameFileNames; unsigned long long lineStart, lineEnd, qlineStart, qlineEnd; - bool flip, allFiles, qtrim, keepforward, createGroup; + bool flip, allFiles, qtrim, keepforward, createGroup, pairedOligos, reorient, logtransform; int numFPrimers, numRPrimers, numLinkers, numSpacers, maxAmbig, maxHomoP, minLength, maxLength, tdiffs, bdiffs, pdiffs, ldiffs, sdiffs; int qWindowSize, qWindowStep, keepFirst, removeLast, count; double qRollAverage, qThreshold, qWindowAverage, qAverage; @@ -112,13 +114,15 @@ struct trimData { map groupCounts; map nameMap; map groupMap; + map pairedBarcodes; + map pairedPrimers; trimData(){} trimData(string fn, string qn, string nf, string cf, string tn, string sn, string tqn, string sqn, string tnn, string snn, string tcn, string scn,string gn, vector > ffn, vector > qfn, vector > nfn, unsigned long long lstart, unsigned long long lend, unsigned long long qstart, unsigned long long qend, MothurOut* mout, - int pd, int bd, int ld, int sd, int td, map pri, map bar, vector revP, vector li, vector spa, + int pd, int bd, int ld, int sd, int td, map pri, map bar, vector revP, vector li, vector spa, map pbr, map ppr, bool po, vector priNameVector, vector barNameVector, bool cGroup, bool aFiles, bool keepF, int keepfi, int removeL, - int WindowStep, int WindowSize, int WindowAverage, bool trim, double Threshold, double Average, double RollAverage, - int minL, int maxA, int maxH, int maxL, bool fli, map nm, map ncount) { + int WindowStep, int WindowSize, int WindowAverage, bool trim, double Threshold, double Average, double RollAverage, bool lt, + int minL, int maxA, int maxH, int maxL, bool fli, bool reo, map nm, map ncount) { filename = fn; qFileName = qn; nameFile = nf; @@ -148,6 +152,9 @@ struct trimData { sdiffs = sd; tdiffs = td; barcodes = bar; + pairedPrimers = ppr; + pairedBarcodes = pbr; + pairedOligos = po; primers = pri; numFPrimers = primers.size(); revPrimer = revP; numRPrimers = revPrimer.size(); linker = li; numLinkers = linker.size(); @@ -167,11 +174,13 @@ struct trimData { qThreshold = Threshold; qAverage = Average; qRollAverage = RollAverage; + logtransform = lt; minLength = minL; maxAmbig = maxA; maxHomoP = maxH; maxLength = maxL; flip = fli; + reorient = reo; nameMap = nm; count = 0; } @@ -251,13 +260,44 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){ } } - - TrimOligos trimOligos(pDataArray->pdiffs, pDataArray->bdiffs, pDataArray->ldiffs, pDataArray->sdiffs, pDataArray->primers, pDataArray->barcodes, pDataArray->revPrimer, pDataArray->linker, pDataArray->spacer); + TrimOligos* trimOligos = NULL; + int numBarcodes = pDataArray->barcodes.size(); + if (pDataArray->pairedOligos) { trimOligos = new TrimOligos(pDataArray->pdiffs, pDataArray->bdiffs, 0, 0, pDataArray->pairedPrimers, pDataArray->pairedBarcodes); numBarcodes = pDataArray->pairedBarcodes.size(); pDataArray->numFPrimers = pDataArray->pairedPrimers.size(); } + else { trimOligos = new TrimOligos(pDataArray->pdiffs, pDataArray->bdiffs, pDataArray->ldiffs, pDataArray->sdiffs, pDataArray->primers, pDataArray->barcodes, pDataArray->revPrimer, pDataArray->linker, pDataArray->spacer); } + + TrimOligos* rtrimOligos = NULL; + if (pDataArray->reorient) { + //create reoriented primer and barcode pairs + map rpairedPrimers, rpairedBarcodes; + for (map::iterator it = pDataArray->pairedPrimers.begin(); it != pDataArray->pairedPrimers.end(); it++) { + oligosPair tempPair(trimOligos->reverseOligo((it->second).reverse), (trimOligos->reverseOligo((it->second).forward))); //reversePrimer, rc ForwardPrimer + rpairedPrimers[it->first] = tempPair; + } + for (map::iterator it = pDataArray->pairedBarcodes.begin(); it != pDataArray->pairedBarcodes.end(); it++) { + oligosPair tempPair(trimOligos->reverseOligo((it->second).reverse), (trimOligos->reverseOligo((it->second).forward))); //reverseBarcode, rc ForwardBarcode + rpairedBarcodes[it->first] = tempPair; + } + + int index = rpairedBarcodes.size(); + for (map::iterator it = pDataArray->barcodes.begin(); it != pDataArray->barcodes.end(); it++) { + oligosPair tempPair("", trimOligos->reverseOligo((it->first))); //reverseBarcode, rc ForwardBarcode + rpairedBarcodes[index] = tempPair; index++; + } + + index = rpairedPrimers.size(); + for (map::iterator it = pDataArray->primers.begin(); it != pDataArray->primers.end(); it++) { + oligosPair tempPair("", trimOligos->reverseOligo((it->first))); //reverseBarcode, rc ForwardBarcode + rpairedPrimers[index] = tempPair; index++; + } + + rtrimOligos = new TrimOligos(pDataArray->pdiffs, pDataArray->bdiffs, 0, 0, rpairedPrimers, rpairedBarcodes); numBarcodes = rpairedBarcodes.size(); + } pDataArray->count = 0; for(int i = 0; i < pDataArray->lineEnd; i++){ //end is the number of sequences to process - if (pDataArray->m->control_pressed) { + if (pDataArray->m->control_pressed) { + delete trimOligos; if (pDataArray->reorient) { delete rtrimOligos; } inFASTA.close(); trimFASTAFile.close(); scrapFASTAFile.close(); if ((pDataArray->createGroup) && (pDataArray->countfile == "")) { outGroupsFile.close(); } if(pDataArray->qFileName != "") { qFile.close(); scrapQualFile.close(); trimQualFile.close(); } @@ -273,11 +313,14 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){ int currentSeqsDiffs = 0; Sequence currSeq(inFASTA); pDataArray->m->gobble(inFASTA); + Sequence savedSeq(currSeq.getName(), currSeq.getAligned()); - QualityScores currQual; + QualityScores currQual; QualityScores savedQual; if(pDataArray->qFileName != ""){ currQual = QualityScores(qFile); pDataArray->m->gobble(qFile); + savedQual.setName(currQual.getName()); savedQual.setScores(currQual.getScores()); } + string origSeq = currSeq.getUnaligned(); if (origSeq != "") { @@ -287,26 +330,26 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){ int primerIndex = 0; if(pDataArray->numLinkers != 0){ - success = trimOligos.stripLinker(currSeq, currQual); + success = trimOligos->stripLinker(currSeq, currQual); if(success > pDataArray->ldiffs) { trashCode += 'k'; } else{ currentSeqsDiffs += success; } } - if(pDataArray->barcodes.size() != 0){ - success = trimOligos.stripBarcode(currSeq, currQual, barcodeIndex); + if(numBarcodes != 0){ + success = trimOligos->stripBarcode(currSeq, currQual, barcodeIndex); if(success > pDataArray->bdiffs) { trashCode += 'b'; } else{ currentSeqsDiffs += success; } } if(pDataArray->numSpacers != 0){ - success = trimOligos.stripSpacer(currSeq, currQual); + success = trimOligos->stripSpacer(currSeq, currQual); if(success > pDataArray->sdiffs) { trashCode += 's'; } else{ currentSeqsDiffs += success; } } if(pDataArray->numFPrimers != 0){ - success = trimOligos.stripForward(currSeq, currQual, primerIndex, pDataArray->keepforward); + success = trimOligos->stripForward(currSeq, currQual, primerIndex, pDataArray->keepforward); if(success > pDataArray->pdiffs) { trashCode += 'f'; } else{ currentSeqsDiffs += success; } } @@ -314,10 +357,48 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){ if (currentSeqsDiffs > pDataArray->tdiffs) { trashCode += 't'; } if(pDataArray->numRPrimers != 0){ - success = trimOligos.stripReverse(currSeq, currQual); + success = trimOligos->stripReverse(currSeq, currQual); if(!success) { trashCode += 'r'; } } + if (pDataArray->reorient && (trashCode != "")) { //if you failed and want to check the reverse + int thisSuccess = 0; + string thisTrashCode = ""; + int thisCurrentSeqsDiffs = 0; + + int thisBarcodeIndex = 0; + int thisPrimerIndex = 0; + + if(numBarcodes != 0){ + thisSuccess = rtrimOligos->stripBarcode(savedSeq, savedQual, thisBarcodeIndex); + if(thisSuccess > pDataArray->bdiffs) { thisTrashCode += 'b'; } + else{ thisCurrentSeqsDiffs += thisSuccess; } + } + + if(pDataArray->numFPrimers != 0){ + thisSuccess = rtrimOligos->stripForward(savedSeq, savedQual, thisPrimerIndex, pDataArray->keepforward); + if(thisSuccess > pDataArray->pdiffs) { thisTrashCode += 'f'; } + else{ thisCurrentSeqsDiffs += thisSuccess; } + } + + if (thisCurrentSeqsDiffs > pDataArray->tdiffs) { thisTrashCode += 't'; } + + if (thisTrashCode == "") { + trashCode = thisTrashCode; + success = thisSuccess; + currentSeqsDiffs = thisCurrentSeqsDiffs; + barcodeIndex = thisBarcodeIndex; + primerIndex = thisPrimerIndex; + savedSeq.reverseComplement(); + currSeq.setAligned(savedSeq.getAligned()); + if(pDataArray->qFileName != ""){ + savedQual.flipQScores(); + currQual.setScores(savedQual.getScores()); + } + }else { trashCode += "(" + thisTrashCode + ")"; } + } + + if(pDataArray->keepFirst != 0){ //success = keepFirstTrim(currSeq, currQual); success = 1; @@ -349,9 +430,9 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){ int origLength = currSeq.getNumBases(); if(pDataArray->qThreshold != 0) { success = currQual.stripQualThreshold(currSeq, pDataArray->qThreshold); } - else if(pDataArray->qAverage != 0) { success = currQual.cullQualAverage(currSeq, pDataArray->qAverage); } - else if(pDataArray->qRollAverage != 0) { success = currQual.stripQualRollingAverage(currSeq, pDataArray->qRollAverage); } - else if(pDataArray->qWindowAverage != 0){ success = currQual.stripQualWindowAverage(currSeq, pDataArray->qWindowStep, pDataArray->qWindowSize, pDataArray->qWindowAverage); } + else if(pDataArray->qAverage != 0) { success = currQual.cullQualAverage(currSeq, pDataArray->qAverage, pDataArray->logtransform); } + else if(pDataArray->qRollAverage != 0) { success = currQual.stripQualRollingAverage(currSeq, pDataArray->qRollAverage, pDataArray->logtransform); } + else if(pDataArray->qWindowAverage != 0){ success = currQual.stripQualWindowAverage(currSeq, pDataArray->qWindowStep, pDataArray->qWindowSize, pDataArray->qWindowAverage, pDataArray->logtransform); } else { success = 1; } //you don't want to trim, if it fails above then scrap it @@ -398,9 +479,9 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){ if(trashCode.length() == 0){ string thisGroup = ""; if (pDataArray->createGroup) { - if(pDataArray->barcodes.size() != 0){ + if(numBarcodes != 0){ thisGroup = pDataArray->barcodeNameVector[barcodeIndex]; - if (pDataArray->primers.size() != 0) { + if (pDataArray->numFPrimers != 0) { if (pDataArray->primerNameVector[primerIndex] != "") { if(thisGroup != "") { thisGroup += "." + pDataArray->primerNameVector[primerIndex]; @@ -438,7 +519,7 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){ } if (pDataArray->createGroup) { - if(pDataArray->barcodes.size() != 0){ + if(numBarcodes != 0){ if (pDataArray->countfile == "") { outGroupsFile << currSeq.getName() << '\t' << thisGroup << endl; } else { pDataArray->groupMap[currSeq.getName()] = thisGroup; } @@ -509,13 +590,14 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){ } //report progress - if((i) % 1000 == 0){ pDataArray->m->mothurOut(toString(i)); pDataArray->m->mothurOutEndLine(); } + if((pDataArray->count) % 1000 == 0){ pDataArray->m->mothurOut(toString(pDataArray->count)); pDataArray->m->mothurOutEndLine(); } } //report progress if((pDataArray->count) % 1000 != 0){ pDataArray->m->mothurOut(toString(pDataArray->count)); pDataArray->m->mothurOutEndLine(); } - + if (pDataArray->reorient) { delete rtrimOligos; } + delete trimOligos; inFASTA.close(); trimFASTAFile.close(); scrapFASTAFile.close();