@@ -18,7 +18,8 @@ setClass("BamTallyParam",

                         variant_strand = "integer",

                         ignore_query_Ns = "logical",

                         indels = "logical",

-                        include_soft_clips = "integer"))

+                        include_soft_clips = "integer",

+                        noncovered = "logical"))

 ### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

 ### Constructor

@@ -39,7 +40,8 @@ BamTallyParam <- function(genome, which = GRanges(),

                           primary_only = FALSE, ignore_duplicates = FALSE,

                           min_depth = 0L, variant_strand = 0L,

                           ignore_query_Ns = FALSE,

-                          indels = FALSE, include_soft_clips = 0L)

+                          indels = FALSE, include_soft_clips = 0L,

+                          noncovered = FALSE)

 {

   if (!is.null(desired_read_group) && !isSingleString(desired_read_group))

     stop("'desired_read_group' must be NULL or a single, non-NA string")

@@ -70,7 +72,7 @@ BamTallyParam <- function(genome, which = GRanges(),

   integer_params <- c("minimum_mapq", "min_depth", "variant_strand",

                       "include_soft_clips")

   params[integer_params] <- lapply(params[integer_params], as.integer)

-  do.call(new, c("BamTallyParam", params))  

+  do.call(new, c("BamTallyParam", params))

 }

 ### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

@@ -195,7 +195,7 @@ normArgTRUEorFALSE <- function(x) {

                          ignore_query_Ns = FALSE,

                          indels = FALSE,

                          blocksize = 1000L, verbosep = FALSE,

-                         include_soft_clips = 0L)

+                         include_soft_clips = 0L, noncovered = FALSE)

 {

   if (!is(bamreader, "GmapBamReader"))

     stop("'bamreader' must be a GmapBamReader")

@@ -217,7 +217,7 @@ normArgTRUEorFALSE <- function(x) {

     if (is.unsorted(read_pos_breaks))

       stop("'read_pos_breaks' must be sorted")

   }

-  .Call(R_Bamtally_iit, bamreader@.extptr, genome_dir, db, which,

+  ptr <- .Call(R_Bamtally_iit, bamreader@.extptr, genome_dir, db, which,

         desired_read_group,

         normArgSingleInteger(alloclength),

         normArgSingleInteger(minimum_mapq),

@@ -233,7 +233,8 @@ normArgTRUEorFALSE <- function(x) {

         normArgTRUEorFALSE(indels),

         normArgSingleInteger(blocksize),

         normArgTRUEorFALSE(verbosep),

-        normArgSingleInteger(include_soft_clips))

+        normArgSingleInteger(include_soft_clips),

+        normArgTRUEorFALSE(noncovered))

 }

 ### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

@@ -7,7 +7,7 @@

 static const R_CallMethodDef callMethods[] = {

   /* bamtally.c */

-  CALLMETHOD_DEF(R_Bamtally_iit, 20),

+  CALLMETHOD_DEF(R_Bamtally_iit, 21),

   CALLMETHOD_DEF(R_tally_iit_parse, 5),

   /* bamreader.c */

@@ -23,7 +23,7 @@ R_Bamtally_iit (SEXP bamreader_R, SEXP genome_dir_R, SEXP db_R,

                 SEXP ignore_query_Ns_p_R,

                 SEXP print_indels_p_R,

                 SEXP blocksize_R, 

-                SEXP verbosep_R, SEXP max_softclip_R)

+                SEXP verbosep_R, SEXP max_softclip_R, SEXP noncovered_R)

 {

   Bamreader_T bamreader = (Bamreader_T) R_ExternalPtrAddr(bamreader_R);

   const char *genome_dir =

@@ -47,6 +47,7 @@ R_Bamtally_iit (SEXP bamreader_R, SEXP genome_dir_R, SEXP db_R,

   int blocksize = asInteger(blocksize_R);

   int verbosep = asLogical(verbosep_R);

   int max_softclip = asInteger(max_softclip_R);

+  int noncovered = asLogical(noncovered_R);

   Genome_T genome = createGenome(genome_dir, db);

   IIT_T chromosome_iit = readChromosomeIIT(genome_dir, db);

@@ -72,7 +73,7 @@ R_Bamtally_iit (SEXP bamreader_R, SEXP genome_dir_R, SEXP db_R,

                                  ignore_duplicates_p,

                                  min_depth, variant_strands, ignore_query_Ns_p,

                                  print_indels_p, blocksize, verbosep,

-                                 /*readlevel_p*/false, max_softclip);

+                                 /*readlevel_p*/false, max_softclip, noncovered);

   IIT_free(&chromosome_iit);

   Genome_free(&genome);

@@ -20,7 +20,7 @@ R_Bamtally_iit (SEXP bamreader_R, SEXP genome_dir_R, SEXP db_R,

                 SEXP ignore_query_Ns_p,

                 SEXP print_indels_p_R,

                 SEXP blocksize_R, 

-                SEXP verbosep_R, SEXP max_softclip_R);

+                SEXP verbosep_R, SEXP max_softclip_R, SEXP noncovered_R);

 SEXP

 R_tally_iit_parse(SEXP tally_iit_R, SEXP cycle_breaks_R,