switched htslib to samtools/htslib master

.gitmodules

@@ -3,8 +3,8 @@
 	url = https://github.com/jwalabroad/fermi-lite
 [submodule "htslib"]
 	path = htslib
-	url = https://github.com/walaj/htslib
-        branch = develop
+	url = https://github.com/samtools/htslib
+        branch = master
 [submodule "bwa"]
 	path = bwa
 	url = https://github.com/jwalabroad/bwa

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

src/BamReader.cpp

@@ -230,7 +230,7 @@ bool BamReader::GetNextRecord(BamRecord& r) {
 
     // try and get the next read
     int32_t status = m_bams.begin()->second.load_read(r);
-    if (status == 0)
+    if (status >= 0)
       return true;
     if (status == -1) {
       // didn't find anything, clear it
@@ -270,7 +270,7 @@ bool BamReader::GetNextRecord(BamRecord& r) {
       tb->empty = true;
       tb->mark_for_closure = true; // no more reads in this BAM
       continue; 
-    } else if (status != 0) { // error sent back from sam_read1
+    } else if (status < 0) { // error sent back from sam_read1
       // run time error
       std::stringstream ss;
       ss << "sam_read1 return status: " << status << " file: " << bam->first;
@@ -328,6 +328,7 @@ std::string BamReader::PrintRegions() const {
 
   if (hts_itr.get() == NULL) {
     valid = sam_read1(fp.get(), m_hdr.get_(), b);    
+
     if (valid < 0) { 
 
 #ifdef DEBUG_WALKER

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)