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Commits on Apr 05, 2016
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mothur-westcott |
79ea058
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42 additions
and 53 deletions.
- +42 −53 source/commands/makecontigscommand.h
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source/commands/makecontigscommand.h
| @@ -233,6 +233,8 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){ | ||
| try { | ||
| unsigned long long numReads = 0; | ||
| pDataArray->delim = '@'; | ||
| + int poundMatchPos = pDataArray->poundMatchPosition; | ||
| + string format = pDataArray->format; | ||
| for (int l = pDataArray->start; l < pDataArray->end; l++) { | ||
| int startTime = time(NULL); | ||
| @@ -254,31 +256,17 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){ | ||
| string forward = ""; string reverse = ""; | ||
| ifstream inForward, inReverse; | ||
| -#ifdef USE_BOOST | ||
| - boost::iostreams::filtering_istream inFF, inRF; | ||
| -#endif | ||
| - if (!gz) { //plain text files | ||
| - m->openInputFile(forwardFile, inForward); | ||
| - m->openInputFile(reverseFile, inReverse); | ||
| - | ||
| - FastqRead fread(inForward, error, format); | ||
| - forward = fread.getName(); | ||
| - | ||
| - FastqRead rread(inReverse, error, format); | ||
| - reverse = rread.getName(); | ||
| - | ||
| - }else { //compressed files | ||
| -#ifdef USE_BOOST | ||
| - m->openInputFileBinary(forwardFile, inForward, inFF); | ||
| - m->openInputFileBinary(reverseFile, inForward, inRF); | ||
| - | ||
| - FastqRead fread(inFF, error, format); | ||
| - forward = fread.getName(); | ||
| - | ||
| - FastqRead rread(inRF, error, format); | ||
| - reverse = rread.getName(); | ||
| -#endif | ||
| - } | ||
| + | ||
| + pDataArray->m->openInputFile(ffastqfile, inForward); | ||
| + pDataArray->m->openInputFile(rfastqfile, inReverse); | ||
| + | ||
| + FastqRead fread(inForward, error, pDataArray->format); | ||
| + forward = fread.getName(); | ||
| + | ||
| + FastqRead rread(inReverse, error, pDataArray->format); | ||
| + reverse = rread.getName(); | ||
| + | ||
| + | ||
| if (forward == reverse) { type = perfectMatch; } | ||
| else { | ||
| @@ -296,7 +284,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){ | ||
| if (tempForward == tempReverse) { type = poundMatch; } | ||
| } | ||
| - nameType = type; | ||
| + pDataArray->nameType = type; | ||
| //////////////////////////////////////////////////////// | ||
| @@ -556,7 +544,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){ | ||
| qual_score[0] = -2; qual_score[1] = -1.58147; qual_score[2] = -0.996843; qual_score[3] = -0.695524; qual_score[4] = -0.507676; qual_score[5] = -0.38013; qual_score[6] = -0.289268; qual_score[7] = -0.222552; qual_score[8] = -0.172557; qual_score[9] = -0.134552; qual_score[10] = -0.105361; qual_score[11] = -0.0827653; qual_score[12] = -0.0651742; qual_score[13] = -0.0514183; qual_score[14] = -0.0406248; qual_score[15] = -0.0321336; qual_score[16] = -0.0254397; qual_score[17] = -0.0201544; qual_score[18] = -0.0159759; qual_score[19] = -0.0126692; qual_score[20] = -0.0100503; qual_score[21] = -0.007975; qual_score[22] = -0.00632956; qual_score[23] = -0.00502447; qual_score[24] = -0.00398902; qual_score[25] = -0.00316729; qual_score[26] = -0.00251505; qual_score[27] = -0.00199726; qual_score[28] = -0.00158615; qual_score[29] = -0.00125972; qual_score[30] = -0.0010005; qual_score[31] = -0.000794644; qual_score[32] = -0.000631156; qual_score[33] = -0.000501313; qual_score[34] = -0.000398186; qual_score[35] = -0.000316278; qual_score[36] = -0.00025122; qual_score[37] = -0.000199546; qual_score[38] = -0.000158502; qual_score[39] = -0.0001259; qual_score[40] = -0.000100005; qual_score[41] = -7.9436e-05; qual_score[42] = -6.30977e-05; qual_score[43] = -5.012e-05; qual_score[44] = -3.98115e-05; qual_score[45] = -3.16233e-05; qual_score[46] = -2.51192e-05; | ||
| int longestBase = 1000; | ||
| - int poundMatchPos = p->poundMatchPosition; | ||
| + int poundMatchPos = pDataArray->poundMatchPosition; | ||
| Alignment* alignment; | ||
| if(pDataArray->align == "gotoh") { alignment = new GotohOverlap(pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch, longestBase); } | ||
| @@ -913,8 +901,8 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){ | ||
| } | ||
| }else { //reading fasta and maybe qual | ||
| - Sequence tfSeq(inFFasta); pDataArray->m->gobble(inFFasta); | ||
| - Sequence trSeq(inRFasta); pDataArray->m->gobble(inRFasta); | ||
| + Sequence fread(inFFasta); pDataArray->m->gobble(inFFasta); | ||
| + Sequence rread(inRFasta); pDataArray->m->gobble(inRFasta); | ||
| ///bool fixed = checkName(fread, rread); | ||
| ////////////////////////////////////////////////////////////// | ||
| bool fixed = false; | ||
| @@ -945,7 +933,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){ | ||
| ///////////////////////////////////////////////////////////// | ||
| if (!fixed) { | ||
| - Sequence tf2Seq(inFFasta); pDataArray->m->gobble(inFFasta); | ||
| + Sequence f2read(inFFasta); pDataArray->m->gobble(inFFasta); | ||
| ///bool fixed = checkName(f2read, rread); | ||
| ////////////////////////////////////////////////////////////// | ||
| fixed = false; | ||
| @@ -975,7 +963,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){ | ||
| }else if (pDataArray->nameType == perfectMatch) { fixed = true; } | ||
| if (!fixed) { | ||
| - Sequence tr2Seq(inRFasta); pDataArray->m->gobble(inRFasta); | ||
| + Sequence r2read(inRFasta); pDataArray->m->gobble(inRFasta); | ||
| ///bool fixed = checkName(fread, r2read); | ||
| ////////////////////////////////////////////////////////////// | ||
| fixed = false; | ||
| @@ -1004,17 +992,17 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){ | ||
| } | ||
| }else if (pDataArray->nameType == perfectMatch) { fixed = true; } | ||
| - if (!fixed) { pDataArray->m->mothurOut("[WARNING]: name mismatch in forward and reverse fastq file. Ignoring, " + tfSeq.getName() + ".\n"); ignore = true; } | ||
| - else { trSeq = tr2Seq; } | ||
| + if (!fixed) { pDataArray->m->mothurOut("[WARNING]: name mismatch in forward and reverse fastq file. Ignoring, " + fread.getName() + ".\n"); ignore = true; } | ||
| + else { rread = r2read; } | ||
| - }else { tfSeq = tf2Seq; } | ||
| + }else { fread = f2read; } | ||
| ///////////////////////////////////////////////////////////// | ||
| } | ||
| - fSeq.setName(tfSeq.getName()); fSeq.setAligned(tfSeq.getAligned()); | ||
| - rSeq.setName(trSeq.getName()); rSeq.setAligned(trSeq.getAligned()); | ||
| + fSeq.setName(fread.getName()); fSeq.setAligned(fread.getAligned()); | ||
| + rSeq.setName(rread.getName()); rSeq.setAligned(rread.getAligned()); | ||
| if (thisfqualindexfile != "") { | ||
| fQual = new QualityScores(inFQualIndex); pDataArray->m->gobble(inFQualIndex); | ||
| rQual = new QualityScores(inRQualIndex); pDataArray->m->gobble(inRQualIndex); | ||
| @@ -1054,10 +1042,10 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){ | ||
| savedFQual = new QualityScores(fQual->getName(), fQual->getQualityScores()); | ||
| savedRQual = new QualityScores(rQual->getName(), rQual->getQualityScores()); | ||
| - if (fQual->getName() != tfSeq.getName()) { pDataArray->m->mothurOut("[WARNING]: name mismatch in forward quality file. Ignoring, " + tfSeq.getName() + ".\n"); ignore = true; } | ||
| - if (rQual->getName() != trSeq.getName()) { pDataArray->m->mothurOut("[WARNING]: name mismatch in reverse quality file. Ignoring, " + trSeq.getName() + ".\n"); ignore = true; } | ||
| + if (fQual->getName() != fread.getName()) { pDataArray->m->mothurOut("[WARNING]: name mismatch in forward quality file. Ignoring, " + fread.getName() + ".\n"); ignore = true; } | ||
| + if (rQual->getName() != rread.getName()) { pDataArray->m->mothurOut("[WARNING]: name mismatch in reverse quality file. Ignoring, " + rread.getName() + ".\n"); ignore = true; } | ||
| } | ||
| - if (tfSeq.getName() != trSeq.getName()) { pDataArray->m->mothurOut("[WARNING]: name mismatch in forward and reverse fasta file. Ignoring, " + tfSeq.getName() + ".\n"); ignore = true; } | ||
| + if (fread.getName() != rread.getName()) { pDataArray->m->mothurOut("[WARNING]: name mismatch in forward and reverse fasta file. Ignoring, " + fread.getName() + ".\n"); ignore = true; } | ||
| } | ||
| }else { | ||
| #ifdef USE_BOOST | ||
| @@ -2193,7 +2181,7 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){ | ||
| */ | ||
| int longestBase = 1000; | ||
| - int poundMatchPos = p->poundMatchPosition; | ||
| + int poundMatchPos = pDataArray->poundMatchPosition; | ||
| Alignment* alignment; | ||
| if(pDataArray->align == "gotoh") { alignment = new GotohOverlap(pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch, longestBase); } | ||
| @@ -2304,6 +2292,7 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){ | ||
| FastqRead rread(inRFasta, ignore, pDataArray->format); pDataArray->m->gobble(inRFasta); | ||
| ///bool fixed = checkName(fread, rread); | ||
| + bool fixed = false; | ||
| ////////////////////////////////////////////////////////////// | ||
| if (pDataArray->nameType == poundMatch) { | ||
| fixed = poundMatch; | ||
| @@ -2543,11 +2532,11 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){ | ||
| } | ||
| }else { //reading fasta and maybe qual | ||
| - Sequence tfSeq(inFFasta); pDataArray->m->gobble(inFFasta); | ||
| - Sequence trSeq(inRFasta); pDataArray->m->gobble(inRFasta); | ||
| + Sequence fread(inFFasta); pDataArray->m->gobble(inFFasta); | ||
| + Sequence rread(inRFasta); pDataArray->m->gobble(inRFasta); | ||
| ///bool fixed = checkName(fread, rread); | ||
| ////////////////////////////////////////////////////////////// | ||
| - fixed = false; | ||
| + bool fixed = false; | ||
| if (pDataArray->nameType == poundMatch) { | ||
| fixed = poundMatch; | ||
| //we know the location of the # matches in the forward and reverse | ||
| @@ -2574,7 +2563,7 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){ | ||
| }else if (pDataArray->nameType == perfectMatch) { fixed = true; } | ||
| ///////////////////////////////////////////////////////////// | ||
| if (!fixed) { | ||
| - Sequence tf2Seq(inFFasta); pDataArray->m->gobble(inFFasta); | ||
| + Sequence f2read(inFFasta); pDataArray->m->gobble(inFFasta); | ||
| ///bool fixed = checkName(f2read, rread); | ||
| ////////////////////////////////////////////////////////////// | ||
| fixed = false; | ||
| @@ -2604,7 +2593,7 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){ | ||
| }else if (pDataArray->nameType == perfectMatch) { fixed = true; } | ||
| if (!fixed) { | ||
| - Sequence tr2Seq(inRFasta); pDataArray->m->gobble(inRFasta); | ||
| + Sequence r2read(inRFasta); pDataArray->m->gobble(inRFasta); | ||
| ///bool fixed = checkName(fread, r2read); | ||
| ////////////////////////////////////////////////////////////// | ||
| fixed = false; | ||
| @@ -2633,17 +2622,17 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){ | ||
| } | ||
| }else if (pDataArray->nameType == perfectMatch) { fixed = true; } | ||
| - if (!fixed) { pDataArray->m->mothurOut("[WARNING]: name mismatch in forward and reverse fastq file. Ignoring, " + tfSeq.getName() + ".\n"); ignore = true; } | ||
| - else { trSeq = tr2Seq; } | ||
| + if (!fixed) { pDataArray->m->mothurOut("[WARNING]: name mismatch in forward and reverse fastq file. Ignoring, " + fread.getName() + ".\n"); ignore = true; } | ||
| + else { rread = r2read; } | ||
| - }else { tfSeq = tf2Seq; } | ||
| + }else { fread = f2read; } | ||
| ///////////////////////////////////////////////////////////// | ||
| } | ||
| - fSeq.setName(tfSeq.getName()); fSeq.setAligned(tfSeq.getAligned()); | ||
| - rSeq.setName(trSeq.getName()); rSeq.setAligned(trSeq.getAligned()); | ||
| + fSeq.setName(fread.getName()); fSeq.setAligned(fread.getAligned()); | ||
| + rSeq.setName(rread.getName()); rSeq.setAligned(rread.getAligned()); | ||
| if (thisfqualindexfile != "") { | ||
| fQual = new QualityScores(inFQualIndex); pDataArray->m->gobble(inFQualIndex); | ||
| rQual = new QualityScores(inRQualIndex); pDataArray->m->gobble(inRQualIndex); | ||
| @@ -2682,10 +2671,10 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){ | ||
| savedFQual = new QualityScores(fQual->getName(), fQual->getQualityScores()); | ||
| savedRQual = new QualityScores(rQual->getName(), rQual->getQualityScores()); | ||
| - if (fQual->getName() != tfSeq.getName()) { pDataArray->m->mothurOut("[WARNING]: name mismatch in forward quality file. Ignoring, " + tfSeq.getName() + ".\n"); ignore = true; } | ||
| - if (rQual->getName() != trSeq.getName()) { pDataArray->m->mothurOut("[WARNING]: name mismatch in reverse quality file. Ignoring, " + trSeq.getName() + ".\n"); ignore = true; } | ||
| + if (fQual->getName() != fread.getName()) { pDataArray->m->mothurOut("[WARNING]: name mismatch in forward quality file. Ignoring, " + fread.getName() + ".\n"); ignore = true; } | ||
| + if (rQual->getName() != rread.getName()) { pDataArray->m->mothurOut("[WARNING]: name mismatch in reverse quality file. Ignoring, " + rread.getName() + ".\n"); ignore = true; } | ||
| } | ||
| - if (tfSeq.getName() != trSeq.getName()) { pDataArray->m->mothurOut("[WARNING]: name mismatch in forward and reverse fasta file. Ignoring, " + tfSeq.getName() + ".\n"); ignore = true; } | ||
| + if (fread.getName() != rread.getName()) { pDataArray->m->mothurOut("[WARNING]: name mismatch in forward and reverse fasta file. Ignoring, " + fread.getName() + ".\n"); ignore = true; } | ||
| } | ||
| int barcodeIndex = 0; | ||