json output

[bamtools.git] / BamMultiReader.h

diff --git a/BamMultiReader.h b/BamMultiReader.h
index 319d3270819c8d0b0d5ed5c288b97193c6f1107a..0464256814f31349b42a0355c438e466308fb99b 100644 (file)
--- a/BamMultiReader.h
+++ b/BamMultiReader.h
@@ -48,7 +48,7 @@ class BamMultiReader {
         bool Jump(int refID, int position = 0);\r
         // opens BAM files (and optional BAM index files, if provided)\r
         //void Open(const vector<std::string&> filenames, const vector<std::string&> indexFilenames);\r
-        void Open(const vector<string> filenames);\r
+        void Open(const vector<string> filenames, bool openIndexes = true);\r
         // returns file pointers to beginning of alignments\r
         bool Rewind(void);\r
 \r
@@ -68,13 +68,15 @@ class BamMultiReader {
         // ----------------------\r
 \r
         // returns unified SAM header text for all files\r
-        const string GetUnifiedHeaderText(void) const;\r
+        const string GetHeaderText(void) const;\r
         // returns number of reference sequences\r
         const int GetReferenceCount(void) const;\r
         // returns vector of reference objects\r
         const BamTools::RefVector GetReferenceData(void) const;\r
         // returns reference id (used for BamMultiReader::Jump()) for the given reference name\r
-        //const int GetReferenceID(const std::string& refName) const;\r
+        const int GetReferenceID(const std::string& refName) const;\r
+        // validates that we have a congruent set of BAM files that are aligned against the same reference sequences\r
+        void ValidateReaders() const;\r
 \r
         // ----------------------\r
         // BAM index operations\r