Move low-level CIGAR utilities to GenomicAlignments package.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@83970 bc3139a8-67e5-0310-9ffc-ced21a209358
RamsinghLab · Dec 6, 2013 · ecd4590 · ecd4590
1 parent 239d664
commit ecd4590
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Showing 12 changed files with 10 additions and 2,403 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -29,7 +29,6 @@ Suggests: AnnotationDbi (>= 1.21.1), AnnotationHub,
 License: Artistic-2.0
 Collate: utils.R
 	phicoef.R
-	cigar-utils.R
 	transcript-utils.R
 	constraint.R
 	makeSeqnameIds.R

diff --git a/NAMESPACE b/NAMESPACE
@@ -1,13 +1,9 @@
 useDynLib(GenomicRanges)
 
 import(methods)
-
 import(utils)  # for as.roman()
-
 importFrom(stats, setNames)
-
 import(BiocGenerics)
-
 import(IRanges)
 
 exportClasses(
@@ -89,25 +85,6 @@ exportMethods(
 export(
     phicoef,
 
-    validCigar,
-    CIGAR_OPS,
-    explodeCigarOps, explodeCigarOpLengths,
-    cigarToRleList,
-    splitCigar,
-    cigarRangesAlongReferenceSpace,
-    cigarRangesAlongQuerySpace,
-    cigarRangesAlongPairwiseSpace,
-    extractAlignmentRangesOnReference,
-    cigarToIRanges,
-    cigarToIRangesListByAlignment, cigarToIRangesListByRName,
-    cigarWidthAlongReferenceSpace,
-    cigarWidthAlongQuerySpace,
-    cigarWidthAlongPairwiseSpace,
-    cigarToWidth, cigarToQWidth,
-    cigarNarrow, cigarQNarrow,
-    cigarOpTable, cigarToCigarTable, summarizeCigarTable,
-    queryLoc2refLoc, queryLocs2refLocs,
-
     makeSeqnameIds,
     Seqinfo,
     GRanges, GRangesList, GenomicRangesList, GIntervalTree,