Merge branch 'master' of https://github.com/walaj/SeqLib

walaj · Apr 25, 2017 · 38c98e3 · 38c98e3
2 parents ad8a854 + c645c4a
commit 38c98e3
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diff --git a/SeqLib/BamRecord.h b/SeqLib/BamRecord.h
@@ -672,6 +672,13 @@ class BamRecord {
    */
   bool GetZTag(const std::string& tag, std::string& s) const;
 
+  /** Get a string of either Z, f or i type. Useful if tag type not known at compile time.
+   * @param tag Name of the tag. eg "XP"
+   * @param s The string to be filled in with the tag information
+   * @return Returns true if the tag is present and is either Z or i, even if empty. Return false if no tag or not Z or i.
+   */  
+  bool GetTag(const std::string& tag, std::string& s) const;
+
   /** Get a vector of type int from a Z tag delimited by "^"
    * Smart-tags allow one to store vectors of strings, ints or doubles in the alignment tags, and
    * do not require an additional data structure on top of bseq1_t. 
@@ -711,6 +718,19 @@ class BamRecord {
     return true;
   }
 
+  /** Get a float (f) tag 
+   * @param tag Name of the tag. eg "AS"
+   * @param t Value to be filled in with the tag value.
+   * @return Return true if the tag exists.
+   */
+  inline bool GetFloatTag(const std::string& tag, float& t) const {
+    uint8_t* p = bam_aux_get(b.get(),tag.c_str());
+    if (!p)
+      return false;
+    t = bam_aux2f(p);
+    return true;
+  }
+
   /** Add a string (Z) tag
    * @param tag Name of the tag. eg "XP"
    * @param val Value for the tag

diff --git a/src/BamRecord.cpp b/src/BamRecord.cpp
@@ -452,6 +452,26 @@ namespace SeqLib {
     bam_aux_append(b.get(), tag.data(), 'Z', val.length()+1, (uint8_t*)val.c_str());
   }
 
+  bool BamRecord::GetTag(const std::string& tag, std::string& s) const {
+    if (GetZTag(tag, s))
+      return true;
+    int32_t t;
+    if (GetIntTag(tag, t)) {
+      std::stringstream ss; 
+      ss << t;
+      s = ss.str();
+      return true;
+    } 
+    float f;
+    if (GetFloatTag(tag, f)) {
+      std::stringstream ss; 
+      ss << f;
+      s = ss.str();
+      return true;
+    }     
+    return false;
+  }
+
   bool BamRecord::GetZTag(const std::string& tag, std::string& s) const {
     uint8_t* p = bam_aux_get(b.get(),tag.c_str());
     if (!p)