Changeset 3334 for trunk/yat/omic/Pileup.h
- Timestamp:
- Oct 23, 2014, 3:26:35 PM (8 years ago)
- File:
-
- 1 edited
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trunk/yat/omic/Pileup.h
r3333 r3334 57 57 58 58 /** 59 Create an Entry with read \a b 59 Create an Entry with read \a b. Entry is initialized to point 60 to first aligned base (b.pos()). 60 61 */ 61 62 Entry(const BamRead& b); … … 144 145 145 146 /** 146 Create a Pileup that will use reads in range [first, last) 147 Create a Pileup that will use reads in range [first, last). The 148 range must be sorted as defined by BamLessPos. 149 150 Iterator is a \readable_iterator. 147 151 */ 148 152 Pileup(Iterator first, Iterator last); … … 169 173 170 174 /** 171 \brief step to next position with coverage 175 \brief step to next position. 176 177 If any Entry has a insertion at current position, increment 178 each Entry that has an insertion. Otherwise increment to next 179 position and update each Entry accordingly. 172 180 */ 173 181 void increment(void); … … 238 246 void Pileup<Iterator>::increment(void) 239 247 { 240 if (data_.empty()) { 241 if (bam_==bam_end_) 242 return; 243 tid_ = bam_->core().tid; 244 pos_ = bam_->core().pos; 245 } 246 else { 247 248 if (!data_.empty()) { 248 249 // in insertion 249 250 if (skip_ref()) { … … 281 282 } 282 283 284 285 // fast forward to next covered locus 286 if (data_.empty()) { 287 if (bam_==bam_end_) 288 return; 289 tid_ = bam_->core().tid; 290 pos_ = bam_->core().pos; 291 } 292 283 293 // read data 284 294 while (bam_!=bam_end_ && bam_->core().tid==tid_ && bam_->pos()<=pos_) {
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