### =========================================================================
 ### GmapBamReader class
 ### -------------------------------------------------------------------------
 ###
 ### The C-level BAM file iterator used by BAM processors in gmap/gstruct.
 ###
 ### This is very similar to BamFile from Rsamtools, but it iterates
 ### line-by-line, not by chunk.
 ###
 
 setClass("GmapBamReader",
          representation(.extptr = "externalptr", path = "character"))
 
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 ### Accessors
 ###
 
 setMethod("path", "GmapBamReader", function(object) object@path)
 
 ## setReplaceMethod("bamWhich", c("GmapBamReader", "ANY"),
 ##                  function(object, value) {

 ##                    bamWhich(object) <- as(value, "IntegerRangesList")

 ##                    object
 ##                  })
 

 ## setReplaceMethod("bamWhich", c("GmapBamReader", "IntegerRangesList"),

 ##                  function(object, value) {
 ##                    if (length(value) != 1L || length(value[[1]]) != 1L)

 ##                      stop("'value' must be an IntegerRangesList with a ",
 ##                           "single, length-one element")

 ##                    .Call(R_Bamread_limit_region, object, names(value),
 ##                          start(value[[1]]), end(value[[1]]))
 ##                  })
 
 ## setReplaceMethod("bamWhich", c("GmapBamReader", "NULL"),
 ##                  function(object, value) {
 ##                    .Call(R_Bamread_unlimit_region, object)
 ##                  })
 
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 ### Constructor
 ###
 
 GmapBamReader <- function(path, which = NULL) {
   if (is(path, "BamFile"))
     path <- path(path)

   if (!isSingleString(path))

     stop("'path' must be a single, non-NA string")
   path <- path.expand(path)
   obj <- new("GmapBamReader", .extptr = .Call(R_Bamread_new, path), path = path)
 ### TODO:
   ##  bamWhich(obj) <- which
   obj
 }
 
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 ### Coercion
 ###
 
 setAs("BamFile", "GmapBamReader", function(from) {
   GmapBamReader(from)
 })
 
 setAs("GmapBamReader", "BamFile", function(from) {
   BamFile(path(from))
 })
 
 
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 ### Show
 ###
 
 setMethod("show", "GmapBamReader", function(object) {
   cat("GmapBamReader object\npath:", path(object), "\n")
 })