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support paired-reads with different lengths. (Thanks to Dr. Hirofumi …
…Nakaoka)
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,7 @@ | ||
| /********************************************************************** | ||
| * Skewer - a fast and accurate adapter trimming tool | ||
| * using the bit-masked k-difference matching algorithm | ||
| * Copyright (c) 2013-2014 by Hongshan Jiang | ||
| * Copyright (c) 2013-2016 by Hongshan Jiang | ||
| * [email protected] | ||
| * | ||
| * If you use this program, please cite the paper: | ||
|
|
@@ -196,6 +196,7 @@ class cStats | |
|
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||
| fpOuts = fpOuts2 = NULL; | ||
| fpMasked = fpMasked2 = NULL; | ||
| fpMask = fpMask2 = NULL; | ||
| fpExcl = fpExcl2 = NULL; | ||
| fpExcluded = fpExcluded2 = NULL; | ||
| nFiles = nFiles2 = 0; | ||
|
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@@ -289,18 +290,10 @@ class cStats | |
| this->fpOut2 = fpOuts2[0].fp; | ||
| this->fpBarcode = fpBarcodes.fp; | ||
| } | ||
| if(fpMasked != NULL) { | ||
| this->fpMask = fpMasked[0].fp; | ||
| } | ||
| if(fpMasked2 != NULL) { | ||
| this->fpMask2 = fpMasked2[0].fp; | ||
| } | ||
| if(fpExcluded != NULL) { | ||
| this->fpExcl = fpExcluded[0].fp; | ||
| } | ||
| if(fpExcluded2 != NULL) { | ||
| this->fpExcl2 = fpExcluded2[0].fp; | ||
| } | ||
| this->fpMask = (fpMasked != NULL) ? fpMasked[0].fp : NULL; | ||
| this->fpMask2 = (fpMasked2 != NULL) ? fpMasked2[0].fp : NULL; | ||
| this->fpExcl = (fpExcluded != NULL) ? fpExcluded[0].fp : NULL; | ||
| this->fpExcl2 = (fpExcluded2 != NULL) ? fpExcluded2[0].fp : NULL; | ||
| this->minAverageQual = (pParameter->minAverageQual > 0) ? (pParameter->baseQual + pParameter->minAverageQual) : 0; | ||
| this->minEndQual = (pParameter->minEndQual > 0) ? (pParameter->baseQual + pParameter->minEndQual) : 0; | ||
| this->minLen = pParameter->minLen; | ||
|
|
@@ -1339,8 +1332,8 @@ void * mt_worker2(void * data) | |
| double cur_ratio; | ||
| int pos, pos2, mLen; | ||
|
|
||
| INDEX idx; | ||
| int rLen, qLen; | ||
| int rLen2, qLen2; | ||
|
|
||
| while(true){ | ||
| while(!pTaskMan->getTask(task)){ | ||
|
|
@@ -1398,24 +1391,26 @@ void * mt_worker2(void * data) | |
| pRecord->tag = TAG_NORMAL; | ||
| rLen = pRecord->seq.n; | ||
| qLen = pRecord->qual.n; | ||
| idx = cMatrix::findAdapterWithPE(pRecord->seq.s, pRecord2->seq.s, rLen, (uchar *)pRecord->qual.s, (uchar *)pRecord2->qual.s, qLen); | ||
| if(idx.pos < 0){ | ||
| idx.pos = 0; | ||
| } | ||
| pos = idx.pos; | ||
| pRecord->idx = pRecord2->idx = idx; | ||
| if(pos < rLen){ // trimmed | ||
| if(pos >= minLen){ | ||
| if(qLen > 0) | ||
| cMatrix::combinePairSeqs(pRecord->seq.s, pRecord2->seq.s, pos, (uchar *)pRecord->qual.s, (uchar *)pRecord2->qual.s, qLen); | ||
| if(pStats->bFilterNs && cMatrix::isBlurry(pRecord->seq.s, pos)){ | ||
| pRecord->tag = pRecord2->tag = TAG_BLURRY; | ||
| rLen2 = pRecord2->seq.n; | ||
| qLen2 = pRecord2->qual.n; | ||
| if(cMatrix::findAdapterWithPE(pRecord->seq.s, pRecord2->seq.s, rLen, rLen2, | ||
| (uchar *)pRecord->qual.s, (uchar *)pRecord2->qual.s, qLen, qLen2, | ||
| pRecord->idx, pRecord2->idx)){ // trimmed | ||
| pos = pRecord->idx.pos; | ||
| pos2 = pRecord2->idx.pos; | ||
| if( (pos >= minLen) && (pos2 >= minLen) ){ | ||
| cMatrix::combinePairSeqs(pRecord->seq.s, pRecord2->seq.s, pos, pos2, | ||
| (uchar *)pRecord->qual.s, (uchar *)pRecord2->qual.s, (int)qLen, (int)qLen2); | ||
| if(pStats->bFilterNs){ | ||
| if(cMatrix::isBlurry(pRecord->seq.s, pos) && cMatrix::isBlurry(pRecord2->seq.s, pos2)){ | ||
| pRecord->tag = pRecord2->tag = TAG_BLURRY; | ||
| } | ||
| } | ||
| } | ||
| } | ||
| else{ | ||
| if(pStats->bFilterNs){ | ||
| if( cMatrix::isBlurry(pRecord->seq.s, rLen) && cMatrix::isBlurry(pRecord2->seq.s, rLen) ){ | ||
| if( cMatrix::isBlurry(pRecord->seq.s, rLen) && cMatrix::isBlurry(pRecord2->seq.s, rLen2) ){ | ||
| pRecord->tag = pRecord2->tag = TAG_BLURRY; | ||
| } | ||
| } | ||
|
|
@@ -1424,7 +1419,7 @@ void * mt_worker2(void * data) | |
| if(pRecord->qual.n > 0) | ||
| pRecord->idx.pos = cMatrix::trimByQuality((uchar *)pRecord->qual.s, min(pos, pRecord->qual.n), minEndQual); | ||
| if(pRecord2->qual.n > 0) | ||
| pRecord2->idx.pos = cMatrix::trimByQuality((uchar *)pRecord2->qual.s, min(pos, pRecord2->qual.n), minEndQual); | ||
| pRecord2->idx.pos = cMatrix::trimByQuality((uchar *)pRecord2->qual.s, min(pos2, pRecord2->qual.n), minEndQual); | ||
| } | ||
| } | ||
|
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||
|
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@@ -2121,8 +2116,8 @@ void * mt_worker2_mp(void * data) | |
| double cur_ratio; | ||
| int pos, pos2; | ||
|
|
||
| INDEX idx; | ||
| int rLen, qLen; | ||
| int rLen2, qLen2; | ||
|
|
||
| while(true){ | ||
| while(!pTaskMan->getTask(task)){ | ||
|
|
@@ -2180,50 +2175,55 @@ void * mt_worker2_mp(void * data) | |
| pRecord->tag = TAG_NORMAL; | ||
| rLen = pRecord->seq.n; | ||
| qLen = pRecord->qual.n; | ||
| idx = cMatrix::findAdapterWithPE(pRecord->seq.s, pRecord2->seq.s, rLen, (uchar *)pRecord->qual.s, (uchar *)pRecord2->qual.s, qLen); | ||
| if(idx.pos < 0){ | ||
| idx.pos = 0; | ||
| } | ||
| pos = idx.pos; | ||
| if(pos < rLen){ // trimmed | ||
| if(pos >= minLen){ | ||
| if(qLen > 0) | ||
| cMatrix::combinePairSeqs(pRecord->seq.s, pRecord2->seq.s, pos, (uchar *)pRecord->qual.s, (uchar *)pRecord2->qual.s, qLen); | ||
| if(pStats->bFilterNs && cMatrix::isBlurry(pRecord->seq.s, pos)){ | ||
| pRecord->tag = pRecord2->tag = TAG_BLURRY; | ||
| rLen2 = pRecord2->seq.n; | ||
| qLen2 = pRecord2->qual.n; | ||
| if(cMatrix::findAdapterWithPE(pRecord->seq.s, pRecord2->seq.s, rLen, rLen2, | ||
| (uchar *)pRecord->qual.s, (uchar *)pRecord2->qual.s, qLen, qLen2, | ||
| pRecord->idx, pRecord2->idx)){ // trimmed | ||
| pos = pRecord->idx.pos; | ||
| pos2 = pRecord2->idx.pos; | ||
| if( (pos >= minLen) && (pos2 >= minLen) ){ | ||
| cMatrix::combinePairSeqs(pRecord->seq.s, pRecord2->seq.s, pos, pos2, | ||
| (uchar *)pRecord->qual.s, (uchar *)pRecord2->qual.s, (int)qLen, (int)qLen2); | ||
| if(pStats->bFilterNs){ | ||
| if( cMatrix::isBlurry(pRecord->seq.s, pos) && cMatrix::isBlurry(pRecord2->seq.s, pos2) ){ | ||
| pRecord->tag = pRecord2->tag = TAG_BLURRY; | ||
| } | ||
| } | ||
| } | ||
| } | ||
| else{ | ||
| pos = rLen; | ||
| pos2 = rLen2; | ||
| if(pStats->bFilterNs){ | ||
| if( cMatrix::isBlurry(pRecord->seq.s, rLen) && cMatrix::isBlurry(pRecord2->seq.s, rLen) ){ | ||
| pRecord->tag = pRecord2->tag = TAG_BLURRY; | ||
| } | ||
| } | ||
| } | ||
| if( (pRecord->tag == TAG_NORMAL) && (pos >= minLen) ) { | ||
| if( (pRecord->tag == TAG_NORMAL) && (pos >= minLen) && (pos2 >= minLen) ) { | ||
| pRecord->idx = cMatrix::findJuncAdapter(pRecord->seq.s, pos, (uchar *)pRecord->qual.s, qLen); | ||
| if(pRecord->idx.pos < 0){ | ||
| pRecord->idx.pos = 0; | ||
| } | ||
| pRecord2->idx = cMatrix::findJuncAdapter(pRecord2->seq.s, pos, (uchar *)pRecord2->qual.s, qLen); | ||
| pRecord2->idx = cMatrix::findJuncAdapter(pRecord2->seq.s, pos2, (uchar *)pRecord2->qual.s, qLen2); | ||
| if(pRecord2->idx.pos < 0){ | ||
| pRecord2->idx.pos = 0; | ||
| } | ||
| if(pos < rLen){ // trimmed | ||
| if( (pos < rLen) || (pos2 < rLen2) ) { // trimmed | ||
| if( (pRecord->idx.bc == 0) || (pRecord2->idx.bc == 0) || (pRecord->idx.bc != pRecord2->idx.bc) ){ | ||
| pRecord->tag = pRecord2->tag = TAG_CONTAMINANT; | ||
| } | ||
| else{ | ||
| if(pRecord->idx.pos + pRecord2->idx.pos + cMatrix::junctionLengths[pRecord->idx.bc] != pos){ | ||
| if(pRecord->idx.pos + pRecord2->idx.pos + cMatrix::junctionLengths[pRecord->idx.bc] != max(pos, pos2)){ | ||
| pRecord->tag = pRecord2->tag = TAG_CONTAMINANT; | ||
| } | ||
| } | ||
| if(minEndQual > 0){ | ||
| if(pRecord->qual.n > 0) | ||
| pRecord->idx.pos = cMatrix::trimByQuality((uchar *)pRecord->qual.s, pRecord->qual.n, minEndQual); | ||
| pRecord->idx.pos = cMatrix::trimByQuality((uchar *)pRecord->qual.s, min(pRecord->idx.pos, pRecord->qual.n), minEndQual); | ||
| if(pRecord2->qual.n > 0) | ||
| pRecord2->idx.pos = cMatrix::trimByQuality((uchar *)pRecord2->qual.s, pRecord2->qual.n, minEndQual); | ||
| pRecord2->idx.pos = cMatrix::trimByQuality((uchar *)pRecord2->qual.s, min(pRecord2->idx.pos, pRecord2->qual.n), minEndQual); | ||
| } | ||
| } | ||
| else{ | ||
|
|
@@ -2286,11 +2286,6 @@ void * mt_worker2_mp(void * data) | |
| } | ||
| } // not case D | ||
| } // pos >= rLen | ||
| pRecord->idx.bc = idx.bc; | ||
| pRecord2->idx.bc = idx.bc; | ||
| } | ||
| else{ // (pRecord->tag != TAG_NORMAL) || (pos < minLen) | ||
| pRecord2->idx = pRecord->idx = idx; | ||
| } | ||
| } | ||
|
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||
|
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@@ -2638,11 +2633,16 @@ int main(int argc, char * argv[]) | |
| return 1; | ||
| } | ||
| } | ||
| para.printVersion(hLog); | ||
| para.printCommandLine(hLog); | ||
| para.printRelatedFiles(hLog); | ||
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| para.printOpt(hLog, true); | ||
| if(!stats.bStdout) para.printOpt(stdout); | ||
| if(!stats.bStdout){ | ||
| para.printLogo(stdout); | ||
| para.printVersion(stdout); | ||
| para.printOpt(stdout); | ||
| } | ||
|
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||
| stats.printTime("started", hLog); | ||
| if(!stats.bStdout) stats.printTime("started", stdout); | ||
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