@@ -15,8 +15,7 @@ Description: This package is to find SNV/Indel differences between two

 License: GPL (>=2)

 LazyLoad: Yes

 Depends: R (>= 3.0.0), methods, Rsamtools (>= 1.18.1), doParallel (>= 1.0.8), Biostrings (>= 2.32.1), stringr (>= 0.6.2), matrixStats

-               (>= 0.10.0), plyr (>= 1.8.3)

-Imports: foreach, IRanges, GenomicRanges

+               (>= 0.10.0), plyr (>= 1.8.3), GenomicRanges (>= 1.22.4), IRanges (>= 2.4.8) 

 Suggests: knitr, RUnit, BiocGenerics

 biocViews: Alignment, Sequencing, Coverage, SequenceMatching, QualityControl, DataImport, Software, SNP, VariantDetection

 VignetteBuilder: knitr

@@ -1,11 +1,10 @@

+import(plyr)

 import(Rsamtools)

 import(doParallel)

 import(methods)

 import(stringr)

 import(Biostrings)

 import(matrixStats)

-import(foreach)

-import(IRanges)

-import(plyr)

 importFrom(GenomicRanges, GRanges)

+importFrom(IRanges,IRanges,shift,breakInChunks)

 export(snpDiff,indelDiff)