deleting SAMFileReader and SAMTruncatedFileReader (#699)

these long deprecated classes were intended to be deleted in #602 but were accidentally resurrected
  updated documentation to point to SamReader instead of SAMFileReader

renamed SAMFileReaderTest to the more accurate SamReaderTest

src/main/java/htsjdk/samtools/BAMIndexer.java

@@ -282,7 +282,7 @@ void startNewReference() {
     /**
      * Generates a BAM index file from an input BAM file
      *
-     * @param reader SAMFileReader for input BAM file
+     * @param reader SamReader for input BAM file
      * @param output File for output index file
      */
     public static void createIndex(SamReader reader, File output) {
@@ -292,7 +292,7 @@ public static void createIndex(SamReader reader, File output) {
     /**
      * Generates a BAM index file from an input BAM file
      *
-     * @param reader SAMFileReader for input BAM file
+     * @param reader SamReader for input BAM file
      * @param output File for output index file
      */
     public static void createIndex(SamReader reader, File output, Log log) {
@@ -310,4 +310,4 @@ public static void createIndex(SamReader reader, File output, Log log) {
         }
         indexer.finish();
     }
-}
+}

src/main/java/htsjdk/samtools/DefaultSAMRecordFactory.java

@@ -1,7 +1,7 @@
 package htsjdk.samtools;
 
 /**
- * Default factory for creating SAM and BAM records used by the SAMFileReader classes.
+ * Default factory for creating SAM and BAM records used by the {@link SamReader} classes.
  *
  * @author Tim Fennell
  */