Changeset 3221

Timestamp:

May 6, 2014, 7:39:36 AM (9 years ago)

Author:

Peter

Message:

deprecate BamRead::cigar(vector<uint32_t>) and provide a new function to set cigar that takes new Aligner::Cigar class.

Location:

branches/0.12-stable

Files:

• NEWS (modified) (1 diff)
• test/bam.cc (modified) (5 diffs)
• yat/omic/BamRead.cc (modified) (2 diffs)
• yat/omic/BamRead.h (modified) (2 diffs)
• yat/utility/deprecate.h (modified) (1 diff)

branches/0.12-stable/NEWS

@@ -6 +6 @@
 
 version 0.12 (released NOT YET)
+  - BamRead::cigar(const std::vector<uint32_t>&) is deprecated
   - Aligner(double, double) is now explicit (see r3207)
   - GetlineIterator(istream&, char) is now explicit (see r3148)

branches/0.12-stable/test/bam.cc

@@ -24 +24 @@
 #include "yat/omic/BamRead.h"
 #endif
+
+#include "yat/utility/Aligner.h"
 
 #include <cassert>
@@ -71 +73 @@
   suite.out() << bam.cigar_str() << "\n";
   OutBamFile os("cigar_test.bam", hdr);
-  std::vector<uint32_t> cig;
+  utility::Aligner::Cigar cig;
 
   bam.cigar(cig);
@@ -78 +80 @@
   os.write(bam);
 
-  cig.resize(1);
-  cig[0] = bam_cigar_gen(bam.sequence_length(), BAM_CMATCH);
+  cig.push_back(BAM_CMATCH, bam.sequence_length());
   bam.cigar(cig);
   suite.out() << bam.cigar_str() << "\n";
@@ -85 +86 @@
   os.write(bam);
 
-  cig.resize(3);
-  cig[0] = bam_cigar_gen(50, BAM_CMATCH);
-  cig[1] = bam_cigar_gen(2, BAM_CDEL);
-  cig[2] = bam_cigar_gen(50, BAM_CMATCH);
+  cig.clear();
+  cig.push_back(BAM_CMATCH, 50);
+  cig.push_back(BAM_CDEL, 2);
+  cig.push_back(BAM_CMATCH, 50);
   bam.cigar(cig);
   suite.out() << bam.cigar_str() << "\n";
@@ -132 +133 @@
 
   // just for consistency
-  std::vector<uint32_t> cig;
+  utility::Aligner::Cigar cig;
   bam.cigar(cig);
   bam.core().flag &= ~BAM_FUNMAP;

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

@@ -149 +149 @@
 
   void BamRead::cigar(const std::vector<uint32_t>& c)
+  {
+    // use the new function cigar(1) to implement this old deprecated variant
+    utility::Aligner::Cigar cig;
+    for (size_t i=0; i<c.size(); ++i)
+      cig.push_back(bam_cigar_op(c[i]), bam_cigar_oplen(c[i]));
+    cigar(cig);
+  }
+
+
+  void BamRead::cigar(const utility::Aligner::Cigar& c)
   {
     int offset = 4*c.size() - 4*core().n_cigar;
@@ -161 +171 @@
 
     // copy new cigar
-    if (c.size())
-      // each cigar element is 4 bytes
-      memcpy(bam1_cigar(bam_), &c[0], 4*c.size());
+    for (size_t i=0; i<c.size(); ++i)
+      bam1_cigar(bam_)[i] = c[i];
+
     bam_->data_len += offset;
     core().n_cigar = c.size();

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

@@ -27 +27 @@
 #include YAT_SAM_HEADER
 
+#include "yat/utility/Aligner.h"
 // This file has to be included to keep compatibility with yat 0.11
-#include <yat/utility/Cigar.h>
+#include "yat/utility/Cigar.h"
+#include "yat/utility/deprecate.h"
 
 #include <functional>
@@ -171 +173 @@
 
        \param c new cigar
+
+       \deprecated Provided for backward compatibility with 0.11
+       API. Use cigar(const utility::Aligner::Cigar&) instead.
     */
-    void cigar(const std::vector<uint32_t>& c);
+    void cigar(const std::vector<uint32_t>& c) YAT_DEPRECATE;
+
+    /**
+       \brief set CIGAR
+
+       \param cigar new cigar
+
+       \since new in yat 0.12
+    */
+    void cigar(const utility::Aligner::Cigar& cigar);
 
     /**

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

@@ -1 +1 @@
 #ifndef _theplu_yat_utility_deprecate_
-#define _theplu_yat_utility_deprecate_ 
+#define _theplu_yat_utility_deprecate_
 
 // $Id$