@@ -1,7 +1,7 @@

 Package: SplicingGraphs

 Title: Create, manipulate, visualize splicing graphs, and assign RNA-seq reads

 	to them

-Version: 1.7.1

+Version: 1.7.2

 Author: D. Bindreither, M. Carlson, M. Morgan, H. Pages

 License: Artistic-2.0

 Description: This package allows the user to create, manipulate, and visualize

@@ -18,7 +18,7 @@ Imports: methods, utils, igraph,

 	 BiocGenerics,

 	 IRanges, GenomicRanges, GenomicFeatures, GenomicAlignments,

 	 graph, Rgraphviz

-Suggests: igraph, Gviz, Rsamtools,

+Suggests: igraph, Gviz, Rsamtools (>= 1.19.17),

 	 TxDb.Hsapiens.UCSC.hg19.knownGene, RNAseqData.HNRNPC.bam.chr14,

 	 RUnit

 Collate: utils.R

@@ -121,7 +121,7 @@ get_TSPC_bam_status <- function(subdir_path, sample_name)

         return(".")

     library(Rsamtools)

     flag0 <- scanBamFlag(#isProperPair=TRUE,

-                         isNotPrimaryRead=FALSE,

+                         isSecondaryAlignment=FALSE,

                          isNotPassingQualityControls=FALSE,

                          isDuplicate=FALSE)

     param0 <- ScanBamParam(flag=flag0, what="flag")

@@ -161,7 +161,7 @@ get_TSPC_bam_gaprate <- function(subdir_path, sample_name)

         return(NA_real_)

     library(Rsamtools)

     flag0 <- scanBamFlag(#isProperPair=TRUE,

-                         isNotPrimaryRead=FALSE,

+                         isSecondaryAlignment=FALSE,

                          isNotPassingQualityControls=FALSE,

                          isDuplicate=FALSE)

     param0 <- ScanBamParam(flag=flag0, what="cigar")

@@ -203,7 +203,7 @@ load_TSPC_bam <- function(subdir_path, sample_name, gapped.reads.only=FALSE)

              "and paired-end reads")

     library(Rsamtools)

     flag0 <- scanBamFlag(#isProperPair=TRUE,

-                         isNotPrimaryRead=FALSE,

+                         isSecondaryAlignment=FALSE,

                          isNotPassingQualityControls=FALSE,

                          isDuplicate=FALSE)

     param0 <- ScanBamParam(flag=flag0, what="mapq")

@@ -14,7 +14,7 @@

 .load_toy_reads <- function()

 {

     library(Rsamtools)

-    flag0 <- scanBamFlag(isNotPrimaryRead=FALSE,

+    flag0 <- scanBamFlag(isSecondaryAlignment=FALSE,

                          isNotPassingQualityControls=FALSE,

                          isDuplicate=FALSE)

     param0 <- ScanBamParam(flag=flag0)

@@ -71,12 +71,12 @@ removeReads(sg)

   will pair them.

   If (b): you can filter out secondary alignments by passing

-  \code{'isNotPrimaryRead=FALSE'} to \code{\link[Rsamtools]{scanBamFlag}}

+  \code{'isSecondaryAlignment=FALSE'} to \code{\link[Rsamtools]{scanBamFlag}}

   when preparing the \link[Rsamtools]{ScanBamParam} object used to load

   the reads. For example:

   \preformatted{

     library(Rsamtools)

-    flag0 <- scanBamFlag(isNotPrimaryRead=FALSE,

+    flag0 <- scanBamFlag(isSecondaryAlignment=FALSE,

                          isNotPassingQualityControls=FALSE,

                          isDuplicate=FALSE)

     param0 <- ScanBamParam(flag=flag0)

@@ -144,7 +144,7 @@ names(sg)

 ## duplicates (see ?scanBamFlag in the Rsamtools package for more

 ## information):

 library(Rsamtools)

-flag0 <- scanBamFlag(isNotPrimaryRead=FALSE,

+flag0 <- scanBamFlag(isSecondaryAlignment=FALSE,

                      isNotPassingQualityControls=FALSE,

                      isDuplicate=FALSE)

 param0 <- ScanBamParam(flag=flag0)

@@ -146,7 +146,7 @@ plot(sgraph(sg["geneD"], tx_id.as.edge.label=TRUE, as.igraph=TRUE))

 ## optical duplicates (see ?scanBamFlag in the Rsamtools package for

 ## more information):

 library(Rsamtools)

-flag0 <- scanBamFlag(isNotPrimaryRead=FALSE,

+flag0 <- scanBamFlag(isSecondaryAlignment=FALSE,

                      isNotPassingQualityControls=FALSE,

                      isDuplicate=FALSE)

 param0 <- ScanBamParam(flag=flag0)

@@ -866,7 +866,7 @@ that we'll pass to \Rfunction{readGAlignmentPairs} (see

 about this):

 <<ScanBamParam>>=

-flag0 <- scanBamFlag(isNotPrimaryRead=FALSE,

+flag0 <- scanBamFlag(isSecondaryAlignment=FALSE,

                      isNotPassingQualityControls=FALSE,

                      isDuplicate=FALSE)

 param0 <- ScanBamParam(flag=flag0)