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#ifndef QUAL_H_ |
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#define QUAL_H_ |
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|
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/* NOTE: This file was written by Ben Langmead, and is borrowed from Bowtie */ |
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|
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#include <stdexcept> |
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#include <iostream> |
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#include "assert_helpers.h" |
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|
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using namespace std; |
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|
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extern unsigned char qualRounds[]; |
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extern unsigned char solToPhred[]; |
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|
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/// Translate a Phred-encoded ASCII character into a Phred quality |
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static inline uint8_t phredCharToPhredQual(char c) { |
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return ((uint8_t)c >= 33 ? ((uint8_t)c - 33) : 0); |
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} |
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|
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/** |
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* Convert a Solexa-scaled quality value into a Phred-scale quality |
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* value. |
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* |
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* p = probability that base is miscalled |
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* Qphred = -10 * log10 (p) |
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* Qsolexa = -10 * log10 (p / (1 - p)) |
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* See: http://en.wikipedia.org/wiki/FASTQ_format |
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* |
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*/ |
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static inline uint8_t solexaToPhred(int sol) { |
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assert_lt(sol, 256); |
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if(sol < -10) return 0; |
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return solToPhred[sol+10]; |
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} |
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|
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class SimplePhredPenalty { |
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public: |
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static uint8_t mmPenalty (uint8_t qual) { |
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return qual; |
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} |
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static uint8_t delPenalty(uint8_t qual) { |
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return qual; |
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} |
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static uint8_t insPenalty(uint8_t qual_left, uint8_t qual_right) { |
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return std::max(qual_left, qual_right); |
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} |
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}; |
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|
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class MaqPhredPenalty { |
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public: |
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static uint8_t mmPenalty (uint8_t qual) { |
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return qualRounds[qual]; |
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} |
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static uint8_t delPenalty(uint8_t qual) { |
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return qualRounds[qual]; |
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} |
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static uint8_t insPenalty(uint8_t qual_left, uint8_t qual_right) { |
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return qualRounds[std::max(qual_left, qual_right)]; |
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} |
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}; |
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|
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static inline uint8_t mmPenalty(bool maq, uint8_t qual) { |
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if(maq) { |
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return MaqPhredPenalty::mmPenalty(qual); |
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} else { |
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return SimplePhredPenalty::mmPenalty(qual); |
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} |
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} |
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|
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static inline uint8_t delPenalty(bool maq, uint8_t qual) { |
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if(maq) { |
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return MaqPhredPenalty::delPenalty(qual); |
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} else { |
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return SimplePhredPenalty::delPenalty(qual); |
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} |
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} |
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|
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static inline uint8_t insPenalty(bool maq, uint8_t qual_left, uint8_t qual_right) { |
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if(maq) { |
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return MaqPhredPenalty::insPenalty(qual_left, qual_right); |
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} else { |
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return SimplePhredPenalty::insPenalty(qual_left, qual_right); |
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} |
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} |
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|
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/** |
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* Take an ASCII-encoded quality value and convert it to a Phred33 |
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* ASCII char. |
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*/ |
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inline static char charToPhred33(char c, bool solQuals, bool phred64Quals) { |
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if(c == ' ') { |
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cerr << "Saw a space but expected an ASCII-encoded quality value." << endl |
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<< "Are quality values formatted as integers? If so, try --integer-quals." << endl; |
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throw 1; |
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} |
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if (solQuals) { |
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// Convert solexa-scaled chars to phred |
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// http://maq.sourceforge.net/fastq.shtml |
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char cc = solexaToPhred((int)c - 64) + 33; |
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if (cc < 33) { |
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cerr << "Saw ASCII character " |
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<< ((int)c) |
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<< " but expected 64-based Solexa qual (converts to " << (int)cc << ")." << endl |
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<< "Try not specifying --solexa-quals." << endl; |
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throw 1; |
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} |
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c = cc; |
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} |
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else if(phred64Quals) { |
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if (c < 64) { |
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cerr << "Saw ASCII character " |
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<< ((int)c) |
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<< " but expected 64-based Phred qual." << endl |
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<< "Try not specifying --solexa1.3-quals/--phred64-quals." << endl; |
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throw 1; |
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} |
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// Convert to 33-based phred |
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c -= (64-33); |
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} |
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else { |
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// Keep the phred quality |
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if (c < 33) { |
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cerr << "Saw ASCII character " |
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<< ((int)c) |
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<< " but expected 33-based Phred qual." << endl; |
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throw 1; |
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} |
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} |
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return c; |
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} |
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|
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/** |
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* Take an integer quality value and convert it to a Phred33 ASCII |
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* char. |
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*/ |
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inline static char intToPhred33(int iQ, bool solQuals) { |
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int pQ; |
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if (solQuals) { |
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// Convert from solexa quality to phred |
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// quality and translate to ASCII |
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// http://maq.sourceforge.net/qual.shtml |
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pQ = solexaToPhred((int)iQ) + 33; |
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} else { |
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// Keep the phred quality and translate |
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// to ASCII |
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pQ = (iQ <= 93 ? iQ : 93) + 33; |
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} |
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if (pQ < 33) { |
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cerr << "Saw negative Phred quality " << ((int)pQ-33) << "." << endl; |
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throw 1; |
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} |
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assert_geq(pQ, 0); |
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return (int)pQ; |
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} |
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|
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#endif /*QUAL_H_*/ |
