Changeset 3334 for trunk/yat/omic/Pileup.h

Timestamp:

Oct 23, 2014, 3:26:35 PM (8 years ago)

Author:

Peter

Message:

Avoid stopping at position one passed a pile, instead fast forward to
next locus with coverage.

refs #806

File:

• trunk/yat/omic/Pileup.h (modified) (5 diffs)

trunk/yat/omic/Pileup.h

@@ -57 +57 @@
 
       /**
-         Create an Entry with read \a b
+         Create an Entry with read \a b. Entry is initialized to point
+         to first aligned base (b.pos()).
        */
       Entry(const BamRead& b);
@@ -144 +145 @@
 
     /**
-       Create a Pileup that will use reads in range [first, last)
+       Create a Pileup that will use reads in range [first, last). The
+       range must be sorted as defined by BamLessPos.
+
+       Iterator is a \readable_iterator.
      */
     Pileup(Iterator first, Iterator last);
@@ -169 +173 @@
 
     /**
-       \brief step to next position with coverage
+       \brief step to next position.
+
+       If any Entry has a insertion at current position, increment
+       each Entry that has an insertion. Otherwise increment to next
+       position and update each Entry accordingly.
      */
     void increment(void);
@@ -238 +246 @@
   void Pileup<Iterator>::increment(void)
   {
-    if (data_.empty()) {
-      if (bam_==bam_end_)
-        return;
-      tid_ = bam_->core().tid;
-      pos_ = bam_->core().pos;
-    }
-    else {
-
+    if (!data_.empty()) {
       // in insertion
       if (skip_ref()) {
@@ -281 +282 @@
     }
 
+
+    // fast forward to next covered locus
+    if (data_.empty()) {
+      if (bam_==bam_end_)
+        return;
+      tid_ = bam_->core().tid;
+      pos_ = bam_->core().pos;
+    }
+
     // read data
     while (bam_!=bam_end_ && bam_->core().tid==tid_ && bam_->pos()<=pos_) {