Changeset 3916

Timestamp:

May 31, 2020, 5:31:11 AM (3 years ago)

Author:

Peter

Message:

avoid incrementing read if it's being removed on the next line. Get rid of comment about speedup; if there is a range of reads to remove it's faster to call list::erase with iterators, but to keep track of that requires book keeping and rarely worth it in the typical case when there are rarely many reads with end position.

File:

• trunk/yat/omic/Pileup.h (modified) (1 diff)

trunk/yat/omic/Pileup.h

@@ -340 +340 @@
         typename std::list<Entry>::iterator read = data_.begin();
         while (read != data_.end()) {
-          read->increment();
           // remove entry if read is entirely left of pos
-          if (read->bam().end() <= pos_) { // FIXME speedup possible
+          if (read->bam().end() <= pos_) {
             data_.erase(read++);
             continue;
           }
+          read->increment();
           // check if we're stepping into insertion
           if (read->cigar_op() == BAM_CINS) {