/usr/include/blasr/format/SAMPrinterImpl.hpp is in libblasr-dev 0~20151014+gitbe5d1bf-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 | #include <algorithm> //max
#include <utility> //swap
#include <assert.h> //assert
using namespace SAMOutput;
template<typename T_Sequence>
void SAMOutput::SetAlignedSequence(T_AlignmentCandidate &alignment, T_Sequence &read,
T_Sequence &alignedSeq,
Clipping clipping) {
//
// In both no, and hard clipping, the dna sequence that is output
// solely corresponds to the aligned sequence.
//
DNALength clippedReadLength = 0;
DNALength clippedStartPos = 0;
if (clipping == none or clipping == hard) {
DNALength qStart = alignment.QAlignStart();
DNALength qEnd = alignment.QAlignEnd();
clippedReadLength = qEnd - qStart;
clippedStartPos = qStart;
}
else if (clipping == soft) {
clippedReadLength = read.length - read.lowQualityPrefix - read.lowQualitySuffix;
clippedStartPos = read.lowQualityPrefix;
}
else if (clipping == subread) {
clippedReadLength = read.SubreadLength();
clippedStartPos = read.SubreadStart();
}
else {
std::cout <<" ERROR! The clipping must be none, hard, subread, or soft when setting the aligned sequence." << std::endl;
assert(0);
}
//
// Set the aligned sequence according to the clipping boundaries.
//
if (alignment.tStrand == 0) {
alignedSeq.ReferenceSubstring(read, clippedStartPos, clippedReadLength);
}
else {
T_Sequence subSeq;
subSeq.ReferenceSubstring(read, clippedStartPos, clippedReadLength);
subSeq.MakeRC(alignedSeq);
assert(alignedSeq.deleteOnExit);
}
}
template<typename T_Sequence>
void SAMOutput::SetSoftClip(T_AlignmentCandidate &alignment,
T_Sequence &read,
DNALength hardClipPrefix,
DNALength hardClipSuffix,
DNALength &softClipPrefix,
DNALength &softClipSuffix) {
DNALength qStart, qEnd;
qStart = alignment.QAlignStart();
qEnd = alignment.QAlignEnd();
assert(qStart >= hardClipPrefix);
softClipPrefix = alignment.QAlignStart() - hardClipPrefix;
assert(alignment.QAlignEnd() + hardClipSuffix <= read.length);
softClipSuffix = read.length - hardClipSuffix - alignment.QAlignEnd();
}
template<typename T_Sequence>
void SAMOutput::SetHardClip(T_AlignmentCandidate &alignment,
T_Sequence &read,
DNALength &prefixClip,
DNALength &suffixClip) {
//
// Set the hard clipping assuming the read is in the forward
// direction.
//
prefixClip = alignment.QAlignStart();
suffixClip = read.length - alignment.QAlignEnd();
if (alignment.tStrand == 1) {
//
// If the read is instead reverse, swap the clipping lengths.
//
std::swap(prefixClip, suffixClip);
}
}
//
// Straight forward: create the cigar string allowing some clipping
// The read is provided to give length and hq information.
//
template<typename T_Sequence>
void SAMOutput::CreateCIGARString(T_AlignmentCandidate &alignment,
T_Sequence &read,
std::string &cigarString,
Clipping clipping,
DNALength & prefixSoftClip, DNALength & suffixSoftClip,
DNALength & prefixHardClip, DNALength & suffixHardClip,
bool cigarUseSeqMatch) {
cigarString = "";
// All cigarString use the no clipping core
std::vector<int> opSize;
std::vector<char> opChar;
CreateNoClippingCigarOps(alignment, opSize, opChar, cigarUseSeqMatch);
// Clipping needs to be added
if (clipping == hard) {
SetHardClip(alignment, read, prefixHardClip, suffixHardClip);
if (prefixHardClip > 0) {
opSize.insert(opSize.begin(), prefixHardClip);
opChar.insert(opChar.begin(), 'H');
}
if (suffixHardClip > 0) {
opSize.push_back(suffixHardClip);
opChar.push_back('H');
}
prefixSoftClip = 0;
suffixSoftClip = 0;
}
if (clipping == soft or clipping == subread) {
//
// Even if clipping is soft, the hard clipping removes the
// low quality regions
//
if (clipping == soft) {
prefixHardClip = read.lowQualityPrefix;
suffixHardClip = read.lowQualitySuffix;
}
else if (clipping == subread) {
prefixHardClip = std::max((DNALength) read.SubreadStart(), read.lowQualityPrefix);
suffixHardClip = std::max((DNALength)(read.length - read.SubreadEnd()), read.lowQualitySuffix);
}
SetSoftClip(alignment, read, prefixHardClip, suffixHardClip, prefixSoftClip, suffixSoftClip);
if (alignment.tStrand == 1) {
std::swap(prefixHardClip, suffixHardClip);
std::swap(prefixSoftClip, suffixSoftClip);
}
//
// Insert the hard and soft clipping so that they are in the
// order H then S if both exist.
//
if (prefixSoftClip > 0) {
opSize.insert(opSize.begin(), prefixSoftClip);
opChar.insert(opChar.begin(), 'S');
}
if (prefixHardClip > 0) {
opSize.insert(opSize.begin(), prefixHardClip);
opChar.insert(opChar.begin(), 'H');
}
//
// Append the hard and soft clipping so they are in the order S
// then H.
//
if (suffixSoftClip > 0) {
opSize.push_back(suffixSoftClip);
opChar.push_back('S');
}
if (suffixHardClip > 0) {
opSize.push_back(suffixHardClip);
opChar.push_back('H');
}
}
CigarOpsToString(opSize, opChar, cigarString);
}
template<typename T_Sequence>
void SAMOutput::PrintAlignment(T_AlignmentCandidate &alignment,
T_Sequence &read,
std::ostream &samFile,
AlignmentContext &context,
SupplementalQVList & qvList,
Clipping clipping,
bool cigarUseSeqMatch) {
std::string cigarString;
uint16_t flag;
T_Sequence alignedSequence;
DNALength prefixSoftClip = 0, suffixSoftClip = 0;
DNALength prefixHardClip = 0, suffixHardClip = 0;
CreateCIGARString(alignment, read, cigarString, clipping, prefixSoftClip, suffixSoftClip, prefixHardClip, suffixHardClip, cigarUseSeqMatch);
SetAlignedSequence(alignment, read, alignedSequence, clipping);
BuildFlag(alignment, context, flag);
samFile << alignment.qName << "\t"
<< flag << "\t"
<< alignment.tName << "\t"; // RNAME
if (alignment.tStrand == 0) {
samFile << alignment.TAlignStart() + 1 << "\t";
// POS, add 1 to get 1 based coordinate system
}
else {
samFile << alignment.tLength - (alignment.TAlignStart() + alignment.TEnd()) + 1 << "\t"; // includes - 1 for rev-comp, +1 for one-based
}
samFile << (int) alignment.mapQV << "\t"// MAPQ
<< cigarString << "\t"; // CIGAR
//
// Determine RNEXT
std::string rNext;
rNext = "*";
/*
if (context.hasNextSubreadPos == false) {
rNext = "*";
}
else {
if (context.rNext == alignment.tName) {
rNext = "=";
}
else {
rNext = context.rNext;
}
}
*/
samFile << rNext << "\t"; // RNEXT
DNALength nextSubreadPos = 0;
/*
if (context.hasNextSubreadPos) {
nextSubreadPos = context.nextSubreadPos + 1;
}*/
samFile << nextSubreadPos << "\t"; // RNEXT, add 1 for 1 based
// indexing
//DNALength tLen = alignment.GenomicTEnd() - alignment.GenomicTBegin();
//SAM v1.5, tLen is set as 0 for single-segment template
samFile << 0 << "\t"; // TLEN
// Print the sequence on one line, and suppress printing the
// newline (by setting the line length to alignedSequence.length
(static_cast<DNASequence*>(&alignedSequence))->PrintSeq(samFile, 0); // SEQ
samFile << "\t";
if (alignedSequence.qual.data != NULL && qvList.useqv == 0) {
alignedSequence.PrintAsciiQual(samFile, 0); // QUAL
}
else {
samFile <<"*";
}
samFile << "\t";
//
// Add optional fields
//
samFile << "RG:Z:" << context.readGroupId << "\t";
samFile << "AS:i:" << alignment.score << "\t";
//
// "RG" read group Id
// "AS" alignment score
// "XS" read alignment start position without counting previous soft clips (1 based)
// "XE" read alignment end position without counting previous soft clips (1 based)
// "XL" aligned read length
// "XQ" query sequence length
// "XT" # of continues reads, always 1 for blasr
// "NM" edit distance
// "FI" read alignment start position (1 based)
//
DNALength qAlignStart = alignment.QAlignStart();
DNALength qAlignEnd = alignment.QAlignEnd();
if (clipping == none) {
samFile << "XS:i:" << qAlignStart + 1 << "\t";
samFile << "XE:i:" << qAlignEnd + 1 << "\t";
}
else if (clipping == hard or clipping == soft or clipping == subread) {
DNALength xs = prefixHardClip;
DNALength xe = read.length - suffixHardClip;
if (alignment.tStrand == 1) {
xs = suffixHardClip;
xe = read.length - prefixHardClip;
}
samFile << "XS:i:" << xs + 1 << "\t"; // add 1 for 1-based indexing in sam
assert(read.length - suffixHardClip == prefixHardClip + alignedSequence.length);
samFile << "XE:i:" << xe + 1 << "\t";
}
samFile << "YS:i:" << read.SubreadStart() << "\t";
samFile << "YE:i:" << read.SubreadEnd() << "\t";
samFile << "ZM:i:" << read.HoleNumber() << "\t";
samFile << "XL:i:" << alignment.qAlignedSeq.length << "\t";
samFile << "XT:i:1\t"; // reads are allways continuous reads, not
// referenced based circular consensus when
// output by blasr.
samFile << "NM:i:" << context.editDist << "\t";
samFile << "FI:i:" << alignment.qAlignedSeqPos + 1;
// Add query sequence length
samFile << "\t" << "XQ:i:" << alignment.qLength;
//
// Write out optional quality values. If qvlist does not
// have any qv's signaled to print, this is a no-op.
//
// First transform characters that are too large to printable ones.
qvList.FormatQVOptionalFields(alignedSequence);
qvList.PrintQVOptionalFields(alignedSequence, samFile);
samFile << std::endl;
}
|