X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=src%2Fapi%2FBamAlignment.h;h=a2349ea9ce9b254066450dc953b99925a8f03b56;hb=c3a7c31347d42a926214e2508d713975d124e8c6;hp=daea418228a7bf4759a946b8aa4d78d64278073f;hpb=25a2a1f6598b6452455da96c28a7f58fd9e7ed2d;p=bamtools.git

diff --git a/src/api/BamAlignment.h b/src/api/BamAlignment.h
index daea418..a2349ea 100644
--- a/src/api/BamAlignment.h
+++ b/src/api/BamAlignment.h
@@ -2,7 +2,7 @@
 // BamAlignment.h (c) 2009 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
 // ---------------------------------------------------------------------------
-// Last modified: 10 October 2011 (DB)
+// Last modified: 16 October 2011 (DB)
 // ---------------------------------------------------------------------------
 // Provides the BamAlignment data structure
 // ***************************************************************************
@@ -10,9 +10,9 @@
 #ifndef BAMALIGNMENT_H
 #define BAMALIGNMENT_H
 
-#include <api/api_global.h>
-#include <api/BamAux.h>
-#include <api/BamConstants.h>
+#include "api/api_global.h"
+#include "api/BamAux.h"
+#include "api/BamConstants.h"
 #include <cstdlib>
 #include <cstring>
 #include <string>
@@ -100,6 +100,12 @@ struct API_EXPORT BamAlignment {
         // returns a description of the last error that occurred
         std::string GetErrorString(void) const;
 
+        // retrieves the size, read locations and reference locations of soft-clip operations
+        bool GetSoftClips(std::vector<int>& clipSizes,
+                          std::vector<int>& readPositions,
+                          std::vector<int>& genomePositions,
+                          bool usePadded = false) const;
+
     // public data fields
     public:
         std::string Name;               // read name
@@ -421,7 +427,7 @@ inline bool BamAlignment::GetTag(const std::string& tag, T& destination) const {
     unsigned int numBytesParsed = 0;
 
     // return failure if tag not found
-    if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) {
+    if ( !FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) {
         // TODO: set error string?
         return false;
     }
@@ -502,7 +508,7 @@ inline bool BamAlignment::GetTag<std::string>(const std::string& tag,
     unsigned int numBytesParsed = 0;
 
     // return failure if tag not found
-    if ( FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) {
+    if ( !FindTag(tag, pTagData, tagDataLength, numBytesParsed) ) {
         // TODO: set error string?
         return false;
     }