Changeset 3213

Timestamp:

May 5, 2014, 9:51:59 AM (9 years ago)

Author:

Peter

Message:

three new cigar functions

Location:

trunk

Files:

• test/cigar.cc (modified) (1 diff)
• yat/utility/Aligner.cc (modified) (2 diffs)
• yat/utility/Aligner.h (modified) (3 diffs)
• yat/utility/Cigar.h (modified) (1 diff)

trunk/test/cigar.cc

@@ -78 +78 @@
   }
 
+  if (!suite.add(cig.length()==17))
+    suite.err() << "error: length: " << cig.length() << " expected 17\n";
+  if (!suite.add(cig.query_length()==16))
+    suite.err() << "error: query length: " << cig.query_length()
+                << " expected 16\n";
+  if (!suite.add(cig.reference_length()==17))
+    suite.err() << "error: length: " << cig.reference_length()
+                << " expected 17\n";
+
   if (!suite.add(cig.op(0)==0))
     suite.err() << "error: cig.op(0): " << cig.op(0) << " expected 0\n";

trunk/yat/utility/Aligner.cc

@@ -169 +169 @@
 
 
+  uint32_t Aligner::Cigar::length(uint8_t mask) const
+  {
+    uint32_t res = 0;
+    for (size_t i=0; i<cigar_.size(); ++i)
+      if (bam_cigar_type(op(i)) & mask)
+        res += oplen(i);
+    return res;
+  }
+
+
+  uint32_t Aligner::Cigar::length(void) const
+  {
+    return length(3);
+  }
+
+
   char Aligner::Cigar::opchr(size_t i) const
   {
@@ -238 +254 @@
 
 
+  uint32_t Aligner::Cigar::query_length(void) const
+  {
+    return length(1);
+  }
+
+
+  uint32_t Aligner::Cigar::reference_length(void) const
+  {
+    return length(2);
+  }
+
+
   size_t Aligner::Cigar::size(void) const
   {

trunk/yat/utility/Aligner.h

@@ -184 +184 @@
 
       /**
+         Total length of operations counting operations that consume
+         either (or both) query and reference e.g. match, insertion,
+         or deletion. HardClip or Padding operations are ignored.
+       */
+      uint32_t length(void) const;
+
+      /**
          See table in class documntation.
 
@@ -226 +233 @@
 
       /**
+         \brief Translate CIGAR to a query length.
+
+         Calculate total length of operations which consume a query
+         e.g. match or insetion. See table in class documentation.
+
+         This is the same function as bam_cigar2qlen in samtools C
+         API.
+       */
+      uint32_t query_length(void) const;
+
+      /**
+         \brief Translate CIGAR to a reference length.
+
+         Calculate total length of operations which consume a reference
+         e.g. match or deletion. See table in class documentation.
+
+         Similar to bam_calend but does not handle \c BAM_CBACK as it has
+         not been included in SAM specification.
+         http://sourceforge.net/p/samtools/mailman/message/29373646/
+       */
+      uint32_t reference_length(void) const;
+
+      /**
          \return cigar element \a i
        */
@@ -237 +267 @@
       std::deque<uint32_t> cigar_;
 
+      // calculate length only counting operations whose type is set
+      // in mask, i.e., mask & type returns true
+      uint32_t length(uint8_t mask) const;
       // using compiler generated copy
       // Cigar(const Cigar& other);

trunk/yat/utility/Cigar.h

@@ -30 +30 @@
 // allow inclusion of config_bam.h so this file is available also without bam.h
 #ifdef YAT_HAVE_LIBBAM
-#include "config_bam.h"
+#include "yat/omic/config_bam.h"
 #include YAT_BAM_HEADER
 #else // if bam.h is not available #define CIGAR