Changeset 3300

Timestamp:

Aug 20, 2014, 7:43:27 AM (9 years ago)

Author:

Peter

Message:

BAM_CBACK is not #defined in older versions of bam.h. refs #810

Location:

branches/0.12-stable/yat

Files:

• omic/BamRead.cc (modified) (3 diffs)
• omic/BamRead.h (modified) (1 diff)
• utility/Cigar.h (modified) (1 diff)

branches/0.12-stable/yat/omic/BamRead.cc

@@ -107 +107 @@
     assert(bam_);
     return bam_->l_aux;
+  }
+
+
+  uint32_t BamRead::calend(const bam1_core_t *c, const uint32_t *cigar) const
+  {
+    int k, end = c->pos;
+    for (k = 0; k < c->n_cigar; ++k) {
+      int op  = bam_cigar_op(cigar[k]);
+      int len = bam_cigar_oplen(cigar[k]);
+      if (op == BAM_CBACK) { // move backward
+        int l, u, v;
+        if (k == c->n_cigar - 1) break; // skip trailing 'B'
+        for (l = k - 1, u = v = 0; l >= 0; --l) {
+          int op1  = bam_cigar_op(cigar[l]);
+          int len1 = bam_cigar_oplen(cigar[l]);
+          if (bam_cigar_type(op1)&1) { // consume query
+            if (u + len1 >= len) { // stop
+              if (bam_cigar_type(op1)&2) v += len - u;
+              break;
+            } else u += len1;
+          }
+          if (bam_cigar_type(op1)&2) v += len1;
+        }
+        end = l < 0? c->pos : end - v;
+      } else if (bam_cigar_type(op)&2) end += bam_cigar_oplen(cigar[k]);
+    }
+    return end;
   }
 
@@ -186 +213 @@
   bam1_core_t& BamRead::core(void)
   { return bam_->core; }
+
+
+  int32_t BamRead::end(void) const
+  {
+    assert(bam_);
+    return this->calend(&core(), bam1_cigar(bam_));
+  }
 
 
@@ -328 +362 @@
 
 
-  int32_t BamRead::end(void) const
-  {
-    assert(bam_);
-    return bam_calend(&core(), bam1_cigar(bam_));
-  }
-
-
   void BamRead::swap(BamRead& other)
   {

branches/0.12-stable/yat/omic/BamRead.h

@@ -309 +309 @@
     friend class OutBamFile;
     friend class BamReadIterator;
+    // FIXME guard out this
+    uint32_t calend(const bam1_core_t *c, const uint32_t *cigar) const;
   };
 

branches/0.12-stable/yat/utility/Cigar.h

@@ -59 +59 @@
 #endif // end of YAT_HAVE_LIBBAM
 
+// CBACK is not defined in old versions of bam.h
+#ifndef BAM_CBACK
+#define BAM_CBACK 9
+#endif
+
 // backport #defines from samtools 0.1.19
 #ifndef BAM_CIGAR_STR