1. gmapR
  2. NAMESPACE
Browse code

The path() generic has moved from Rsamtools to BiocGenerics

LiNk-NY authored on 20/12/2017 20:04:28
Showing 1 changed files
NAMESPACE
History View file @ c67b519
... ... 
@@ -1,6 +1,7 @@
1 1 
 useDynLib(gmapR, .registration = TRUE)
2 2
3 
-importFrom(Rsamtools, path, bamPaths, "bamWhich<-", BamFile, BamFileList,
3 
+importFrom(BiocGenerics, path)
4 
+importFrom(Rsamtools, bamPaths, "bamWhich<-", BamFile, BamFileList,
4 5 
            BamSampler)
5 6 
 importFrom(tools, file_path_as_absolute, file_ext, file_path_sans_ext,
6 7 
            list_files_with_exts)
... ... 
@@ -12,7 +13,8 @@ import(GenomicRanges)
12 13 
 import(GenomeInfoDb)
13 14 
 import(BiocParallel)
14 15 
 importMethodsFrom(GenomeInfoDb, genome)
15 
-importFrom(utils, packageVersion)
16 
+importFrom(stats, setNames)
17 
+importFrom(utils, packageVersion, read.table, str)
16 18 
 importFrom(Biostrings, getSeq, readDNAStringSet, DNAStringSet)
17 19 
 importMethodsFrom(GenomicRanges, seqnames, strand)
18 20 
 importMethodsFrom(Rsamtools, asBam)
Browse code

export and document cmetindex command

Michael Lawrence authored on 14/11/2017 22:43:33
Showing 1 changed files
NAMESPACE
History View file @ 1cb2c80
... ... 
@@ -34,7 +34,7 @@ importMethodsFrom(GenomicAlignments, qwidth)
34 34 
 export(bam_tally, GmapGenome, GmapGenomeDirectory, GsnapParam,
35 35 
        directory, BamTallyParam, makeGmapGenomePackage, GsnapOutput,
36 36 
        GmapSnps, GmapSnpDirectory, TP53Genome, TP53Which, variantSummary,
37 
-       GmapParam)
37 
+       GmapParam, cmetindex)
38 38
39 39 
 exportClasses(GmapGenome, GmapGenomeDirectory, GmapSnpDirectory,
40 40 
               GsnapOutput, GmapSnps, BamTallyParam, GsnapParam, GmapParam,
Browse code

general cleanup and fixes, doc updates

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@111183 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 03/12/2015 21:11:09
Showing 1 changed files
NAMESPACE
History View file @ f053c5f
... ... 
@@ -17,12 +17,13 @@ importFrom(Biostrings, getSeq, readDNAStringSet, DNAStringSet)
17 17 
 importMethodsFrom(GenomicRanges, seqnames, strand)
18 18 
 importMethodsFrom(Rsamtools, asBam)
19 19 
 importClassesFrom(GenomicFeatures, TxDb)
20 
-importFrom(GenomicFeatures, transcripts, exons)
20 
+importFrom(GenomicFeatures, transcripts, exons, exonsBy)
21 21 
 importClassesFrom(rtracklayer, RTLFile, FastaFile, RTLFileList)
22 
-importFrom(rtracklayer, "referenceSequence<-", import, export, FastaFile)
22 
+importFrom(rtracklayer, "referenceSequence<-", import, export, FastaFile,
23 
+           FileForFormat)
23 24 
 importMethodsFrom(rtracklayer, export)
24 25 
 importFrom(VariantAnnotation, readVcf, ScanVcfParam, fixed, VRanges, ref, alt,
25 
-           "ref<-", "alt<-", altDepth, refDepth)
26 
+           "ref<-", "alt<-", altDepth, refDepth, "vcfWhich<-")
26 27 
 importClassesFrom(VariantAnnotation, "VCF", "VRanges")
27 28 
 importFrom(BSgenome, getSeq, providerVersion)
28 29 
 importFrom(GenomicAlignments, readGAlignments)
Browse code

add ability to call GMAP

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@110840 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 23/11/2015 23:25:34
Showing 1 changed files
NAMESPACE
History View file @ ead94b3
... ... 
@@ -18,7 +18,7 @@ importMethodsFrom(GenomicRanges, seqnames, strand)
18 18 
 importMethodsFrom(Rsamtools, asBam)
19 19 
 importClassesFrom(GenomicFeatures, TxDb)
20 20 
 importFrom(GenomicFeatures, transcripts, exons)
21 
-importClassesFrom(rtracklayer, RTLFile, FastaFile)
21 
+importClassesFrom(rtracklayer, RTLFile, FastaFile, RTLFileList)
22 22 
 importFrom(rtracklayer, "referenceSequence<-", import, export, FastaFile)
23 23 
 importMethodsFrom(rtracklayer, export)
24 24 
 importFrom(VariantAnnotation, readVcf, ScanVcfParam, fixed, VRanges, ref, alt,
... ... 
@@ -32,10 +32,14 @@ importMethodsFrom(GenomicAlignments, qwidth)
32 32
33 33 
 export(bam_tally, GmapGenome, GmapGenomeDirectory, GsnapParam,
34 34 
        directory, BamTallyParam, makeGmapGenomePackage, GsnapOutput,
35 
-       GmapSnps, GmapSnpDirectory, TP53Genome, TP53Which, variantSummary)
35 
+       GmapSnps, GmapSnpDirectory, TP53Genome, TP53Which, variantSummary,
36 
+       GmapParam)
36 37
37 38 
 exportClasses(GmapGenome, GmapGenomeDirectory, GmapSnpDirectory,
38 
-              GsnapOutput, GmapSnps, BamTallyParam, GsnapParam)
39 
+              GsnapOutput, GmapSnps, BamTallyParam, GsnapParam, GmapParam,
40 
+              GmapAlignerParam)
39 41
40 42 
 exportMethods(bamPaths, path, genome, seqinfo, gsnap, "snps<-",
41 
-              "spliceSites<-", getSeq)
43 
+              "spliceSites<-", getSeq, gmap)
44 
+
45 
+S3method(as.list, GmapAlignerParam)
Browse code

resurrect improvements that we reverted before the April release, expect breakage for a while

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@110039 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 28/10/2015 18:51:00
Showing 1 changed files
NAMESPACE
History View file @ 8418591
... ... 
@@ -11,10 +11,12 @@ import(methods)
11 11 
 import(GenomicRanges)
12 12 
 import(GenomeInfoDb)
13 13 
 import(BiocParallel)
14 
+importMethodsFrom(GenomeInfoDb, genome)
14 15 
 importFrom(utils, packageVersion)
15 16 
 importFrom(Biostrings, getSeq, readDNAStringSet, DNAStringSet)
17 
+importMethodsFrom(GenomicRanges, seqnames, strand)
16 18 
 importMethodsFrom(Rsamtools, asBam)
17 
-importClassesFrom(GenomicFeatures, TxDb) #TranscriptDb)
19 
+importClassesFrom(GenomicFeatures, TxDb)
18 20 
 importFrom(GenomicFeatures, transcripts, exons)
19 21 
 importClassesFrom(rtracklayer, RTLFile, FastaFile)
20 22 
 importFrom(rtracklayer, "referenceSequence<-", import, export, FastaFile)
Browse code

Reverted to r101133, along with NAMESPACE fixes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@102487 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 14/04/2015 21:40:44
Showing 1 changed files
NAMESPACE
History View file @ d5ed124
... ... 
@@ -11,12 +11,10 @@ import(methods)
11 11 
 import(GenomicRanges)
12 12 
 import(GenomeInfoDb)
13 13 
 import(BiocParallel)
14 
-importMethodsFrom(GenomeInfoDb, genome)
15 14 
 importFrom(utils, packageVersion)
16 15 
 importFrom(Biostrings, getSeq, readDNAStringSet, DNAStringSet)
17 
-importMethodsFrom(GenomicRanges, seqnames, strand)
18 16 
 importMethodsFrom(Rsamtools, asBam)
19 
-importClassesFrom(GenomicFeatures, TxDb)
17 
+importClassesFrom(GenomicFeatures, TxDb) #TranscriptDb)
20 18 
 importFrom(GenomicFeatures, transcripts, exons)
21 19 
 importClassesFrom(rtracklayer, RTLFile, FastaFile)
22 20 
 importFrom(rtracklayer, "referenceSequence<-", import, export, FastaFile)
Browse code

screw it, just import all of GenomeInfoDb

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@101254 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 26/03/2015 23:26:42
Showing 1 changed files
NAMESPACE
History View file @ c9319fc
... ... 
@@ -9,11 +9,11 @@ import(IRanges)
9 9 
 import(S4Vectors)
10 10 
 import(methods)
11 11 
 import(GenomicRanges)
12 
+import(GenomeInfoDb)
12 13 
 import(BiocParallel)
13 14 
 importMethodsFrom(GenomeInfoDb, genome)
14 15 
 importFrom(utils, packageVersion)
15 16 
 importFrom(Biostrings, getSeq, readDNAStringSet, DNAStringSet)
16 
-importFrom(GenomeInfoDb, seqinfo, seqlengths, Seqinfo)
17 17 
 importMethodsFrom(GenomicRanges, seqnames, strand)
18 18 
 importMethodsFrom(Rsamtools, asBam)
19 19 
 importClassesFrom(GenomicFeatures, TxDb)
Browse code

import Seqinfo from GenomeInfoDb

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@101253 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 26/03/2015 23:22:03
Showing 1 changed files
NAMESPACE
History View file @ ca61e3d
... ... 
@@ -13,7 +13,7 @@ import(BiocParallel)
13 13 
 importMethodsFrom(GenomeInfoDb, genome)
14 14 
 importFrom(utils, packageVersion)
15 15 
 importFrom(Biostrings, getSeq, readDNAStringSet, DNAStringSet)
16 
-importFrom(GenomeInfoDb, seqinfo, seqlengths)
16 
+importFrom(GenomeInfoDb, seqinfo, seqlengths, Seqinfo)
17 17 
 importMethodsFrom(GenomicRanges, seqnames, strand)
18 18 
 importMethodsFrom(Rsamtools, asBam)
19 19 
 importClassesFrom(GenomicFeatures, TxDb)
Browse code

import seqinfo and seqlengths from GenomeInfoDb

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@101190 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 25/03/2015 23:20:27
Showing 1 changed files
NAMESPACE
History View file @ 3f46e6a
... ... 
@@ -13,10 +13,10 @@ import(BiocParallel)
13 13 
 importMethodsFrom(GenomeInfoDb, genome)
14 14 
 importFrom(utils, packageVersion)
15 15 
 importFrom(Biostrings, getSeq, readDNAStringSet, DNAStringSet)
16 
-importFrom(GenomicRanges, seqinfo)
16 
+importFrom(GenomeInfoDb, seqinfo, seqlengths)
17 17 
 importMethodsFrom(GenomicRanges, seqnames, strand)
18 18 
 importMethodsFrom(Rsamtools, asBam)
19 
-importClassesFrom(GenomicFeatures, TxDb) #TranscriptDb)
19 
+importClassesFrom(GenomicFeatures, TxDb)
20 20 
 importFrom(GenomicFeatures, transcripts, exons)
21 21 
 importClassesFrom(rtracklayer, RTLFile, FastaFile)
22 22 
 importFrom(rtracklayer, "referenceSequence<-", import, export, FastaFile)
Browse code

add codon tally support. No vbump yet

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@93316 bc3139a8-67e5-0310-9ffc-ced21a209358

Gabriel Becker authored on 11/08/2014 23:42:48
Showing 1 changed files
NAMESPACE
History View file @ c78be69
... ... 
@@ -1,20 +1,22 @@
1 1 
 useDynLib(gmapR, .registration = TRUE)
2 2
3 
-import(methods)
4 
-importFrom(tools, file_path_as_absolute, file_ext, file_path_sans_ext,
5 
-           list_files_with_exts)
6 
-importFrom(utils, packageVersion)
7 
-
8 3 
 importFrom(Rsamtools, path, bamPaths, "bamWhich<-", BamFile, BamFileList,
9 4 
            BamSampler)
5 
+importFrom(tools, file_path_as_absolute, file_ext, file_path_sans_ext,
6 
+           list_files_with_exts)
10 7 
 importFrom(Biobase, createPackage)
11 
-import(S4Vectors)
12 8 
 import(IRanges)
13 
-import(GenomeInfoDb)
9 
+import(S4Vectors)
10 
+import(methods)
14 11 
 import(GenomicRanges)
12 
+import(BiocParallel)
13 
+importMethodsFrom(GenomeInfoDb, genome)
14 
+importFrom(utils, packageVersion)
15 15 
 importFrom(Biostrings, getSeq, readDNAStringSet, DNAStringSet)
16 
+importFrom(GenomicRanges, seqinfo)
17 
+importMethodsFrom(GenomicRanges, seqnames, strand)
16 18 
 importMethodsFrom(Rsamtools, asBam)
17 
-importClassesFrom(GenomicFeatures, TxDb)
19 
+importClassesFrom(GenomicFeatures, TxDb) #TranscriptDb)
18 20 
 importFrom(GenomicFeatures, transcripts, exons)
19 21 
 importClassesFrom(rtracklayer, RTLFile, FastaFile)
20 22 
 importFrom(rtracklayer, "referenceSequence<-", import, export, FastaFile)
Browse code

follow renaming of TranscriptDb class -> TxDb

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@92976 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 28/07/2014 23:15:59
Showing 1 changed files
NAMESPACE
History View file @ c0cce6c
... ... 
@@ -14,7 +14,7 @@ import(GenomeInfoDb)
14 14 
 import(GenomicRanges)
15 15 
 importFrom(Biostrings, getSeq, readDNAStringSet, DNAStringSet)
16 16 
 importMethodsFrom(Rsamtools, asBam)
17 
-importClassesFrom(GenomicFeatures, TranscriptDb)
17 
+importClassesFrom(GenomicFeatures, TxDb)
18 18 
 importFrom(GenomicFeatures, transcripts, exons)
19 19 
 importClassesFrom(rtracklayer, RTLFile, FastaFile)
20 20 
 importFrom(rtracklayer, "referenceSequence<-", import, export, FastaFile)
Browse code

resync with latest changes in GenomicRanges/GenomeInfoDb

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@89880 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 02/05/2014 23:12:32
Showing 1 changed files
NAMESPACE
History View file @ 6cca01e
... ... 
@@ -1,18 +1,18 @@
1 1 
 useDynLib(gmapR, .registration = TRUE)
2 2
3 
-importFrom(Rsamtools, path, bamPaths, "bamWhich<-", BamFile, BamFileList,
4 
-           BamSampler)
3 
+import(methods)
5 4 
 importFrom(tools, file_path_as_absolute, file_ext, file_path_sans_ext,
6 5 
            list_files_with_exts)
6 
+importFrom(utils, packageVersion)
7 
+
8 
+importFrom(Rsamtools, path, bamPaths, "bamWhich<-", BamFile, BamFileList,
9 
+           BamSampler)
7 10 
 importFrom(Biobase, createPackage)
8 11 
 import(S4Vectors)
9 12 
 import(IRanges)
10 
-import(methods)
13 
+import(GenomeInfoDb)
11 14 
 import(GenomicRanges)
12 
-importFrom(utils, packageVersion)
13 15 
 importFrom(Biostrings, getSeq, readDNAStringSet, DNAStringSet)
14 
-importFrom(GenomicRanges, genome, seqinfo)
15 
-importMethodsFrom(GenomicRanges, seqnames, strand)
16 16 
 importMethodsFrom(Rsamtools, asBam)
17 17 
 importClassesFrom(GenomicFeatures, TranscriptDb)
18 18 
 importFrom(GenomicFeatures, transcripts, exons)
Browse code

resync with stuff moving from IRanges to S4Vectors

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@89179 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 18/04/2014 15:04:25
Showing 1 changed files
NAMESPACE
History View file @ f7ab666
... ... 
@@ -5,6 +5,7 @@ importFrom(Rsamtools, path, bamPaths, "bamWhich<-", BamFile, BamFileList,
5 5 
 importFrom(tools, file_path_as_absolute, file_ext, file_path_sans_ext,
6 6 
            list_files_with_exts)
7 7 
 importFrom(Biobase, createPackage)
8 
+import(S4Vectors)
8 9 
 import(IRanges)
9 10 
 import(methods)
10 11 
 import(GenomicRanges)
Browse code

drop the unique read position counts; renamed count.pos/count.neg to count.plus/count.minus (way better names)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@88417 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 04/04/2014 13:36:22
Showing 1 changed files
NAMESPACE
History View file @ 30f3bfd
... ... 
@@ -1,6 +1,7 @@
1 1 
 useDynLib(gmapR, .registration = TRUE)
2 2
3 
-importFrom(Rsamtools, path, bamPaths, "bamWhich<-", BamFile, BamFileList)
3 
+importFrom(Rsamtools, path, bamPaths, "bamWhich<-", BamFile, BamFileList,
4 
+           BamSampler)
4 5 
 importFrom(tools, file_path_as_absolute, file_ext, file_path_sans_ext,
5 6 
            list_files_with_exts)
6 7 
 importFrom(Biobase, createPackage)
... ... 
@@ -21,6 +22,8 @@ importFrom(VariantAnnotation, readVcf, ScanVcfParam, fixed, VRanges, ref, alt,
21 22 
            "ref<-", "alt<-", altDepth, refDepth)
22 23 
 importClassesFrom(VariantAnnotation, "VCF", "VRanges")
23 24 
 importFrom(BSgenome, getSeq, providerVersion)
25 
+importFrom(GenomicAlignments, readGAlignments)
26 
+importMethodsFrom(GenomicAlignments, qwidth)
24 27
25 28 
 ## public API
26 29
Browse code

TP53 genome is now named by the TxDb package from which the TP53 region was retrieved, so that it is automatically refreshed with annotation changes, and devel and release can coexist.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@87282 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 10/03/2014 23:10:51
Showing 1 changed files
NAMESPACE
History View file @ fab13f0
... ... 
@@ -7,6 +7,7 @@ importFrom(Biobase, createPackage)
7 7 
 import(IRanges)
8 8 
 import(methods)
9 9 
 import(GenomicRanges)
10 
+importFrom(utils, packageVersion)
10 11 
 importFrom(Biostrings, getSeq, readDNAStringSet, DNAStringSet)
11 12 
 importFrom(GenomicRanges, genome, seqinfo)
12 13 
 importMethodsFrom(GenomicRanges, seqnames, strand)
Browse code

import altDepth/refDepth

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@86409 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 13/02/2014 18:55:50
Showing 1 changed files
NAMESPACE
History View file @ 9b877fe
... ... 
@@ -17,7 +17,7 @@ importClassesFrom(rtracklayer, RTLFile, FastaFile)
17 17 
 importFrom(rtracklayer, "referenceSequence<-", import, export, FastaFile)
18 18 
 importMethodsFrom(rtracklayer, export)
19 19 
 importFrom(VariantAnnotation, readVcf, ScanVcfParam, fixed, VRanges, ref, alt,
20 
-           "ref<-", "alt<-")
20 
+           "ref<-", "alt<-", altDepth, refDepth)
21 21 
 importClassesFrom(VariantAnnotation, "VCF", "VRanges")
22 22 
 importFrom(BSgenome, getSeq, providerVersion)
23 23
Browse code

better to not import readBamGappedAlignments at all (it's defunct)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@83107 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 08/11/2013 22:10:44
Showing 1 changed files
NAMESPACE
History View file @ 6b077cc
... ... 
@@ -1,7 +1,6 @@
1 1 
 useDynLib(gmapR, .registration = TRUE)
2 2
3 3 
 importFrom(Rsamtools, path, bamPaths, "bamWhich<-", BamFile, BamFileList)
4 
-importFrom(GenomicAlignments, readBamGappedAlignments)
5 4 
 importFrom(tools, file_path_as_absolute, file_ext, file_path_sans_ext,
6 5 
            list_files_with_exts)
7 6 
 importFrom(Biobase, createPackage)
Browse code

Import readGAlignmentsFromBam from new GenomicAlignments package instead of Rsamtools (even though gmapR doesn't seem to use it internally).

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@83106 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 08/11/2013 22:07:43
Showing 1 changed files
NAMESPACE
History View file @ f561cd9
... ... 
@@ -1,7 +1,7 @@
1 1 
 useDynLib(gmapR, .registration = TRUE)
2 2
3 
-importFrom(Rsamtools, path, bamPaths, readBamGappedAlignments, "bamWhich<-",
4 
-           BamFile, BamFileList)
3 
+importFrom(Rsamtools, path, bamPaths, "bamWhich<-", BamFile, BamFileList)
4 
+importFrom(GenomicAlignments, readBamGappedAlignments)
5 5 
 importFrom(tools, file_path_as_absolute, file_ext, file_path_sans_ext,
6 6 
            list_files_with_exts)
7 7 
 importFrom(Biobase, createPackage)
Browse code

renamed summarizeVariants to variantSummary the which in GsnapParam is now a GenomicRanges instead of a RangesList refactor the show method of BamTallyParam to rely on showAsCell

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@78525 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 15/07/2013 23:41:54
Showing 1 changed files
NAMESPACE
History View file @ f3db568
... ... 
@@ -26,7 +26,7 @@ importFrom(BSgenome, getSeq, providerVersion)
26 26
27 27 
 export(bam_tally, GmapGenome, GmapGenomeDirectory, GsnapParam,
28 28 
        directory, BamTallyParam, makeGmapGenomePackage, GsnapOutput,
29 
-       GmapSnps, GmapSnpDirectory, TP53Genome, TP53Which, summarizeVariants)
29 
+       GmapSnps, GmapSnpDirectory, TP53Genome, TP53Which, variantSummary)
30 30
31 31 
 exportClasses(GmapGenome, GmapGenomeDirectory, GmapSnpDirectory,
32 32 
               GsnapOutput, GmapSnps, BamTallyParam, GsnapParam)
Browse code

Refactor bam_tally, so that bam_tally returns a TallyIIT object, which is then summarized via summarizeVariants; this allows computing tallies once and summarizing them in different ways (like maybe get the coverage). The summarizeVariants function yields a VRanges.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@78427 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 14/07/2013 00:43:43
Showing 1 changed files
NAMESPACE
History View file @ 59c3684
... ... 
@@ -6,6 +6,7 @@ importFrom(tools, file_path_as_absolute, file_ext, file_path_sans_ext,
6 6 
            list_files_with_exts)
7 7 
 importFrom(Biobase, createPackage)
8 8 
 import(IRanges)
9 
+import(methods)
9 10 
 import(GenomicRanges)
10 11 
 importFrom(Biostrings, getSeq, readDNAStringSet, DNAStringSet)
11 12 
 importFrom(GenomicRanges, genome, seqinfo)
... ... 
@@ -16,15 +17,16 @@ importFrom(GenomicFeatures, transcripts, exons)
16 17 
 importClassesFrom(rtracklayer, RTLFile, FastaFile)
17 18 
 importFrom(rtracklayer, "referenceSequence<-", import, export, FastaFile)
18 19 
 importMethodsFrom(rtracklayer, export)
19 
-importFrom(VariantAnnotation, readVcf, ScanVcfParam, fixed)
20 
-importClassesFrom(VariantAnnotation, "VCF")
20 
+importFrom(VariantAnnotation, readVcf, ScanVcfParam, fixed, VRanges, ref, alt,
21 
+           "ref<-", "alt<-")
22 
+importClassesFrom(VariantAnnotation, "VCF", "VRanges")
21 23 
 importFrom(BSgenome, getSeq, providerVersion)
22 24
23 25 
 ## public API
24 26
25 27 
 export(bam_tally, GmapGenome, GmapGenomeDirectory, GsnapParam,
26 28 
        directory, BamTallyParam, makeGmapGenomePackage, GsnapOutput,
27 
-       GmapSnps, GmapSnpDirectory, TP53Genome, TP53Which)
29 
+       GmapSnps, GmapSnpDirectory, TP53Genome, TP53Which, summarizeVariants)
28 30
29 31 
 exportClasses(GmapGenome, GmapGenomeDirectory, GmapSnpDirectory,
30 32 
               GsnapOutput, GmapSnps, BamTallyParam, GsnapParam)
Browse code

Use readDNAStringSet() instead of read.DNAStringSet().

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@76521 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 13/05/2013 23:23:36
Showing 1 changed files
NAMESPACE
History View file @ 0dbb11f
... ... 
@@ -7,7 +7,7 @@ importFrom(tools, file_path_as_absolute, file_ext, file_path_sans_ext,
7 7 
 importFrom(Biobase, createPackage)
8 8 
 import(IRanges)
9 9 
 import(GenomicRanges)
10 
-importFrom(Biostrings, getSeq, read.DNAStringSet, DNAStringSet)
10 
+importFrom(Biostrings, getSeq, readDNAStringSet, DNAStringSet)
11 11 
 importFrom(GenomicRanges, genome, seqinfo)
12 12 
 importMethodsFrom(GenomicRanges, seqnames, strand)
13 13 
 importMethodsFrom(Rsamtools, asBam)
Browse code

import 'exons'

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@75072 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 30/03/2013 02:36:06
Showing 1 changed files
NAMESPACE
History View file @ 82c0838
... ... 
@@ -12,7 +12,7 @@ importFrom(GenomicRanges, genome, seqinfo)
12 12 
 importMethodsFrom(GenomicRanges, seqnames, strand)
13 13 
 importMethodsFrom(Rsamtools, asBam)
14 14 
 importClassesFrom(GenomicFeatures, TranscriptDb)
15 
-importFrom(GenomicFeatures, transcripts)
15 
+importFrom(GenomicFeatures, transcripts, exons)
16 16 
 importClassesFrom(rtracklayer, RTLFile, FastaFile)
17 17 
 importFrom(rtracklayer, "referenceSequence<-", import, export, FastaFile)
18 18 
 importMethodsFrom(rtracklayer, export)
Browse code

Add GmapGenome->DNAStringSet coercion, exports the whole genome sequence. This means export(x, "genome.fasta") should work.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@74945 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 27/03/2013 19:11:09
Showing 1 changed files
NAMESPACE
History View file @ 2f697ca
... ... 
@@ -7,7 +7,7 @@ importFrom(tools, file_path_as_absolute, file_ext, file_path_sans_ext,
7 7 
 importFrom(Biobase, createPackage)
8 8 
 import(IRanges)
9 9 
 import(GenomicRanges)
10 
-importFrom(Biostrings, getSeq, read.DNAStringSet)
10 
+importFrom(Biostrings, getSeq, read.DNAStringSet, DNAStringSet)
11 11 
 importFrom(GenomicRanges, genome, seqinfo)
12 12 
 importMethodsFrom(GenomicRanges, seqnames, strand)
13 13 
 importMethodsFrom(Rsamtools, asBam)
Browse code

Export new stuff, bump version

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@74876 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 26/03/2013 21:44:37
Showing 1 changed files
NAMESPACE
History View file @ 248ed95
... ... 
@@ -18,6 +18,7 @@ importFrom(rtracklayer, "referenceSequence<-", import, export, FastaFile)
18 18 
 importMethodsFrom(rtracklayer, export)
19 19 
 importFrom(VariantAnnotation, readVcf, ScanVcfParam, fixed)
20 20 
 importClassesFrom(VariantAnnotation, "VCF")
21 
+importFrom(BSgenome, getSeq, providerVersion)
21 22
22 23 
 ## public API
23 24
... ... 
@@ -29,4 +30,4 @@ exportClasses(GmapGenome, GmapGenomeDirectory, GmapSnpDirectory,
29 30 
               GsnapOutput, GmapSnps, BamTallyParam, GsnapParam)
30 31
31 32 
 exportMethods(bamPaths, path, genome, seqinfo, gsnap, "snps<-",
32 
-              "spliceSites<-")
33 
+              "spliceSites<-", getSeq)
Browse code

drop import of parallel package, as we apparently do not use it?

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@69966 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 29/09/2012 04:03:09
Showing 1 changed files
NAMESPACE
History View file @ 7afec90
... ... 
@@ -7,7 +7,6 @@ importFrom(tools, file_path_as_absolute, file_ext, file_path_sans_ext,
7 7 
 importFrom(Biobase, createPackage)
8 8 
 import(IRanges)
9 9 
 import(GenomicRanges)
10 
-import(parallel)
11 10 
 importFrom(Biostrings, getSeq, read.DNAStringSet)
12 11 
 importFrom(GenomicRanges, genome, seqinfo)
13 12 
 importMethodsFrom(GenomicRanges, seqnames, strand)
Browse code

Export TP53Which()

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@69355 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 12/09/2012 05:15:05
Showing 1 changed files
NAMESPACE
History View file @ 3dd29e4
... ... 
@@ -24,8 +24,7 @@ importClassesFrom(VariantAnnotation, "VCF")
24 24
25 25 
 export(bam_tally, GmapGenome, GmapGenomeDirectory, GsnapParam,
26 26 
        directory, BamTallyParam, makeGmapGenomePackage, GsnapOutput,
27 
-       GmapSnps, GmapSnpDirectory, TP53Genome, subsetRegion, getGeneRoi,
28 
-       checkPackageInstalled)
27 
+       GmapSnps, GmapSnpDirectory, TP53Genome, TP53Which)
29 28
30 29 
 exportClasses(GmapGenome, GmapGenomeDirectory, GmapSnpDirectory,
31 30 
               GsnapOutput, GmapSnps, BamTallyParam, GsnapParam)
Browse code

*gmapR option name for returning system calls is now "systemCallMode"

*asSystemCall.R added

*previous code that calls .system had to account for the case of when
getOption("systemCallMode") is TRUE. Since exception is now being
thrown, this logic was removed from gsnap() function

*LungCancerLines no longer mentioned in NAMESPACE


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@69338 bc3139a8-67e5-0310-9ffc-ced21a209358

Cory Barr authored on 11/09/2012 22:12:30
Showing 1 changed files
NAMESPACE
History View file @ 297de88
... ... 
@@ -8,7 +8,6 @@ importFrom(Biobase, createPackage)
8 8 
 import(IRanges)
9 9 
 import(GenomicRanges)
10 10 
 import(parallel)
11 
-import(LungCancerLines)
12 11 
 importFrom(Biostrings, getSeq, read.DNAStringSet)
13 12 
 importFrom(GenomicRanges, genome, seqinfo)
14 13 
 importMethodsFrom(GenomicRanges, seqnames, strand)
Browse code

added capability to overwrite .system via providing a function to options('gmapRSysCall')

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@69298 bc3139a8-67e5-0310-9ffc-ced21a209358

Cory Barr authored on 11/09/2012 02:32:47
Showing 1 changed files
NAMESPACE
History View file @ 1116df9
... ... 
@@ -8,6 +8,7 @@ importFrom(Biobase, createPackage)
8 8 
 import(IRanges)
9 9 
 import(GenomicRanges)
10 10 
 import(parallel)
11 
+import(LungCancerLines)
11 12 
 importFrom(Biostrings, getSeq, read.DNAStringSet)
12 13 
 importFrom(GenomicRanges, genome, seqinfo)
13 14 
 importMethodsFrom(GenomicRanges, seqnames, strand)
Browse code

added patches supplied by Greg

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@69292 bc3139a8-67e5-0310-9ffc-ced21a209358

Cory Barr authored on 10/09/2012 22:52:34
Showing 1 changed files
NAMESPACE
History View file @ 9dfa7ad
... ... 
@@ -24,7 +24,8 @@ importClassesFrom(VariantAnnotation, "VCF")
24 24
25 25 
 export(bam_tally, GmapGenome, GmapGenomeDirectory, GsnapParam,
26 26 
        directory, BamTallyParam, makeGmapGenomePackage, GsnapOutput,
27 
-       GmapSnps, GmapSnpDirectory, TP53Genome)
27 
+       GmapSnps, GmapSnpDirectory, TP53Genome, subsetRegion, getGeneRoi,
28 
+       checkPackageInstalled)
28 29
29 30 
 exportClasses(GmapGenome, GmapGenomeDirectory, GmapSnpDirectory,
30 31 
               GsnapOutput, GmapSnps, BamTallyParam, GsnapParam)
Browse code

Fix typo in spliceSites<-

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@69202 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 07/09/2012 17:05:26
Showing 1 changed files
NAMESPACE
History View file @ 1e5e275
... ... 
@@ -30,4 +30,4 @@ exportClasses(GmapGenome, GmapGenomeDirectory, GmapSnpDirectory,
30 30 
               GsnapOutput, GmapSnps, BamTallyParam, GsnapParam)
31 31
32 32 
 exportMethods(bamPaths, path, genome, seqinfo, gsnap, "snps<-",
33 
-              "spliteSites<-")
33 
+              "spliceSites<-")
Browse code

Fix import of getSeq

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@69201 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 07/09/2012 17:02:06
Showing 1 changed files
NAMESPACE
History View file @ e35b784
... ... 
@@ -8,7 +8,7 @@ importFrom(Biobase, createPackage)
8 8 
 import(IRanges)
9 9 
 import(GenomicRanges)
10 10 
 import(parallel)
11 
-import(Biostrings, getSeq, read.DNAStringSet)
11 
+importFrom(Biostrings, getSeq, read.DNAStringSet)
12 12 
 importFrom(GenomicRanges, genome, seqinfo)
13 13 
 importMethodsFrom(GenomicRanges, seqnames, strand)
14 14 
 importMethodsFrom(Rsamtools, asBam)
Browse code

Add a GRangesList spliceSites<- method. Seems like it is working, but more testing is needed.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@69198 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 07/09/2012 16:50:04
Showing 1 changed files
NAMESPACE
History View file @ 5fdf642
... ... 
@@ -29,4 +29,5 @@ export(bam_tally, GmapGenome, GmapGenomeDirectory, GsnapParam,
29 29 
 exportClasses(GmapGenome, GmapGenomeDirectory, GmapSnpDirectory,
30 30 
               GsnapOutput, GmapSnps, BamTallyParam, GsnapParam)
31 31
32 
-exportMethods(bamPaths, path, genome, seqinfo, gsnap, "snps<-")
32 
+exportMethods(bamPaths, path, genome, seqinfo, gsnap, "snps<-",
33 
+              "spliteSites<-")
Browse code

Add TP53Genome function

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@69157 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 06/09/2012 23:14:14
Showing 1 changed files
NAMESPACE
History View file @ 2256145
... ... 
@@ -7,12 +7,13 @@ importFrom(tools, file_path_as_absolute, file_ext, file_path_sans_ext,
7 7 
 importFrom(Biobase, createPackage)
8 8 
 import(IRanges)
9 9 
 import(GenomicRanges)
10 
-import(Biostrings)
11 10 
 import(parallel)
11 
+import(Biostrings, getSeq, read.DNAStringSet)
12 12 
 importFrom(GenomicRanges, genome, seqinfo)
13 13 
 importMethodsFrom(GenomicRanges, seqnames, strand)
14 14 
 importMethodsFrom(Rsamtools, asBam)
15 15 
 importClassesFrom(GenomicFeatures, TranscriptDb)
16 
+importFrom(GenomicFeatures, transcripts)
16 17 
 importClassesFrom(rtracklayer, RTLFile, FastaFile)
17 18 
 importFrom(rtracklayer, "referenceSequence<-", import, export, FastaFile)
18 19 
 importMethodsFrom(rtracklayer, export)
... ... 
@@ -23,7 +24,7 @@ importClassesFrom(VariantAnnotation, "VCF")
23 24
24 25 
 export(bam_tally, GmapGenome, GmapGenomeDirectory, GsnapParam,
25 26 
        directory, BamTallyParam, makeGmapGenomePackage, GsnapOutput,
26 
-       GmapSnps, GmapSnpDirectory)
27 
+       GmapSnps, GmapSnpDirectory, TP53Genome)
27 28
28 29 
 exportClasses(GmapGenome, GmapGenomeDirectory, GmapSnpDirectory,
29 30 
               GsnapOutput, GmapSnps, BamTallyParam, GsnapParam)
Browse code

exporting GmapSnps and GmapSnpDirectory

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@68698 bc3139a8-67e5-0310-9ffc-ced21a209358

Cory Barr authored on 21/08/2012 23:52:09
Showing 1 changed files
NAMESPACE
History View file @ 0a4b811
... ... 
@@ -23,11 +23,9 @@ importClassesFrom(VariantAnnotation, "VCF")
23 23
24 24 
 export(bam_tally, GmapGenome, GmapGenomeDirectory, GsnapParam,
25 25 
        directory, BamTallyParam, makeGmapGenomePackage, GsnapOutput,
26 
-       flankingCycleBreaks)
26 
+       GmapSnps, GmapSnpDirectory)
27 
+
27 28 
 exportClasses(GmapGenome, GmapGenomeDirectory, GmapSnpDirectory,
28 29 
               GsnapOutput, GmapSnps, BamTallyParam, GsnapParam)
29 
-exportMethods(bamPaths, path, genome, seqinfo, gsnap)
30 
-
31 
-## gsnap API
32 30
33 
-## export("snps<-", getDefaultGmapGenomePath)
31 
+exportMethods(bamPaths, path, genome, seqinfo, gsnap, "snps<-")
Browse code

Add missing imports, export flankingCycleBins utility.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@68557 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 17/08/2012 20:25:21
Showing 1 changed files
NAMESPACE
History View file @ d99f805
... ... 
@@ -1,8 +1,9 @@
1 1 
 useDynLib(gmapR, .registration = TRUE)
2 2
3 3 
 importFrom(Rsamtools, path, bamPaths, readBamGappedAlignments, "bamWhich<-",
4 
-           BamFile)
5 
-importFrom(tools, file_path_as_absolute, file_ext, file_path_sans_ext)
4 
+           BamFile, BamFileList)
5 
+importFrom(tools, file_path_as_absolute, file_ext, file_path_sans_ext,
6 
+           list_files_with_exts)
6 7 
 importFrom(Biobase, createPackage)
7 8 
 import(IRanges)
8 9 
 import(GenomicRanges)
... ... 
@@ -21,7 +22,8 @@ importClassesFrom(VariantAnnotation, "VCF")
21 22 
 ## public API
22 23
23 24 
 export(bam_tally, GmapGenome, GmapGenomeDirectory, GsnapParam,
24 
-       directory, BamTallyParam, makeGmapGenomePackage, GsnapOutput)
25 
+       directory, BamTallyParam, makeGmapGenomePackage, GsnapOutput,
26 
+       flankingCycleBreaks)
25 27 
 exportClasses(GmapGenome, GmapGenomeDirectory, GmapSnpDirectory,
26 28 
               GsnapOutput, GmapSnps, BamTallyParam, GsnapParam)
27 29 
 exportMethods(bamPaths, path, genome, seqinfo, gsnap)
Browse code

renaming gmapR2 to gmapR: it lives again

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@68172 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 02/08/2012 22:24:24
Showing 1 changed files
NAMESPACE
History View file @ b22faf0
... ... 
@@ -1,25 +1,31 @@
1 
-importFrom(Rsamtools, path, bamPaths, readBamGappedAlignments)
2 
-importFrom(tools, list_files_with_exts)
1 
+useDynLib(gmapR, .registration = TRUE)
2 
+
3 
+importFrom(Rsamtools, path, bamPaths, readBamGappedAlignments, "bamWhich<-",
4 
+           BamFile)
5 
+importFrom(tools, file_path_as_absolute, file_ext, file_path_sans_ext)
6 
+importFrom(Biobase, createPackage)
3 7 
 import(IRanges)
4 8 
 import(GenomicRanges)
5 9 
 import(Biostrings)
6 10 
 import(parallel)
11 
+importFrom(GenomicRanges, genome, seqinfo)
12 
+importMethodsFrom(GenomicRanges, seqnames, strand)
13 
+importMethodsFrom(Rsamtools, asBam)
14 
+importClassesFrom(GenomicFeatures, TranscriptDb)
15 
+importClassesFrom(rtracklayer, RTLFile, FastaFile)
16 
+importFrom(rtracklayer, "referenceSequence<-", import, export, FastaFile)
17 
+importMethodsFrom(rtracklayer, export)
18 
+importFrom(VariantAnnotation, readVcf, ScanVcfParam, fixed)
19 
+importClassesFrom(VariantAnnotation, "VCF")
20 
+
21 
+## public API
22 
+
23 
+export(bam_tally, GmapGenome, GmapGenomeDirectory, GsnapParam,
24 
+       directory, BamTallyParam, makeGmapGenomePackage, GsnapOutput)
25 
+exportClasses(GmapGenome, GmapGenomeDirectory, GmapSnpDirectory,
26 
+              GsnapOutput, GmapSnps, BamTallyParam, GsnapParam)
27 
+exportMethods(bamPaths, path, genome, seqinfo, gsnap)
7 28
8 
-export(buildGmapDbSNPIndex)
9 
-export(buildGmapIITFromFasta)
10 
-export(buildGmapIndex)
11 
-export(buildGsnapSNPIIT)
12 
-export(buildRefseqSpliceSites)
13 
-export(consolidateGmapFiles)
14 
-export(consolidateGsnapFiles)
15 
-export(exonsToGmapSpliceSites)
16 
-export(getGsnapFileCounts)
17 
-export(globals)
18 
-export(installGmap)
19 
-export(parallelized_gsnap)
20 
-export(tally2GR)
21 
-export(tallyInDel)
22 
-export(getChrGRangesFromGmap)
29 
+## gsnap API
23 30
24 
-exportClasses(GsnapOutput)
25 
-export(GsnapOutput, bamPaths)
31 
+## export("snps<-", getDefaultGmapGenomePath)
Browse code

if bam_tally not found, an exception is thrown

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@65646 bc3139a8-67e5-0310-9ffc-ced21a209358

Cory Barr authored on 02/05/2012 00:43:22
Showing 1 changed files
NAMESPACE
History View file @ 138fd12
... ... 
@@ -1,4 +1,5 @@
1 1 
 importFrom(Rsamtools, path, bamPaths, readBamGappedAlignments)
2 
+importFrom(tools, list_files_with_exts)
2 3 
 import(IRanges)
3 4 
 import(GenomicRanges)
4 5 
 import(Biostrings)
Browse code

modified the tally2GR function to take a GRanges for the position, can nor break the genome into smaller chunks or tally a single base of interest. Also moved getChrGRangesFromGmap.R from SNVsOmuC to here and bumped the version

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@64512 bc3139a8-67e5-0310-9ffc-ced21a209358

Jeremiah Degenhardt authored on 27/03/2012 23:03:30
Showing 1 changed files
NAMESPACE
History View file @ ef5f44a
... ... 
@@ -18,6 +18,7 @@ export(installGmap)
18 18 
 export(parallelized_gsnap)
19 19 
 export(tally2GR)
20 20 
 export(tallyInDel)
21 
+export(getChrGRangesFromGmap)
21 22
22 23 
 exportClasses(GsnapOutput)
23 24 
 export(GsnapOutput, bamPaths)
Browse code

fixed a bug in the tallyInDel

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@63997 bc3139a8-67e5-0310-9ffc-ced21a209358

Jeremiah Degenhardt authored on 15/03/2012 23:06:21
Showing 1 changed files
NAMESPACE
History View file @ 841d14a
... ... 
@@ -1,4 +1,4 @@
1 
-importFrom(Rsamtools, path, bamPaths)
1 
+importFrom(Rsamtools, path, bamPaths, readBamGappedAlignments)
2 2 
 import(IRanges)
3 3 
 import(GenomicRanges)
4 4 
 import(Biostrings)
Browse code

added a function to tally indels from bam_tally added it to exports and bumped the version

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@63977 bc3139a8-67e5-0310-9ffc-ced21a209358

Jeremiah Degenhardt authored on 15/03/2012 18:27:39
Showing 1 changed files
NAMESPACE
History View file @ c8ae1d3
... ... 
@@ -17,6 +17,7 @@ export(globals)
17 17 
 export(installGmap)
18 18 
 export(parallelized_gsnap)
19 19 
 export(tally2GR)
20 
+export(tallyInDel)
20 21
21 22 
 exportClasses(GsnapOutput)
22 23 
 export(GsnapOutput, bamPaths)
Browse code

now imports parallel

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@62315 bc3139a8-67e5-0310-9ffc-ced21a209358

Jeremiah Degenhardt authored on 26/01/2012 23:14:24
Showing 1 changed files
NAMESPACE
History View file @ 6a4f72c
... ... 
@@ -2,6 +2,7 @@ importFrom(Rsamtools, path, bamPaths)
2 2 
 import(IRanges)
3 3 
 import(GenomicRanges)
4 4 
 import(Biostrings)
5 
+import(parallel)
5 6
6 7 
 export(buildGmapDbSNPIndex)
7 8 
 export(buildGmapIITFromFasta)
Browse code

Export our bamPaths generic. WARNING: roxygen will overwrite this.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@62230 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 23/01/2012 23:26:43
Showing 1 changed files
NAMESPACE
History View file @ 16122e3
... ... 
@@ -18,4 +18,4 @@ export(parallelized_gsnap)
18 18 
 export(tally2GR)
19 19
20 20 
 exportClasses(GsnapOutput)
21 
-export(GsnapOutput)
21 
+export(GsnapOutput, bamPaths)
Browse code

Document and output GsnapOutput()

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@62229 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 23/01/2012 23:02:30
Showing 1 changed files
NAMESPACE
History View file @ 4474368
... ... 
@@ -18,3 +18,4 @@ export(parallelized_gsnap)
18 18 
 export(tally2GR)
19 19
20 20 
 exportClasses(GsnapOutput)
21 
+export(GsnapOutput)
Browse code

Temporarily export GnsapOutput class from gmapR; will get erased when we run Roxygen.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@62224 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 23/01/2012 22:07:15
Showing 1 changed files
NAMESPACE
History View file @ cc3f47c
... ... 
@@ -16,3 +16,5 @@ export(globals)
16 16 
 export(installGmap)
17 17 
 export(parallelized_gsnap)
18 18 
 export(tally2GR)
19 
+
20 
+exportClasses(GsnapOutput)
Browse code

Just import IRanges, GenomicRanges and Biostrings

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@62150 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 19/01/2012 19:43:00
Showing 1 changed files
NAMESPACE
History View file @ 97bf6d3
... ... 
@@ -1,5 +1,7 @@
1 1 
 importFrom(Rsamtools, path, bamPaths)
2 
-importFrom(IRanges, isSingleString)
2 
+import(IRanges)
3 
+import(GenomicRanges)
4 
+import(Biostrings)
3 5
4 6 
 export(buildGmapDbSNPIndex)
5 7 
 export(buildGmapIITFromFasta)
Browse code

Import isSingleString from IRanges

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@62149 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 19/01/2012 18:17:11
Showing 1 changed files
NAMESPACE
History View file @ c68fa70
... ... 
@@ -1,4 +1,5 @@
1 1 
 importFrom(Rsamtools, path, bamPaths)
2 
+importFrom(IRanges, isSingleString)
2 3
3 4 
 export(buildGmapDbSNPIndex)
4 5 
 export(buildGmapIITFromFasta)
Browse code

Add tally functions

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@61526 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 21/12/2011 22:34:25
Showing 1 changed files
NAMESPACE
History View file @ 04980de
... ... 
@@ -12,3 +12,4 @@ export(getGsnapFileCounts)
12 12 
 export(globals)
13 13 
 export(installGmap)
14 14 
 export(parallelized_gsnap)
15 
+export(tally2GR)
Browse code

Fix installation problem (needed path from Rsamtools) and demonstrate use of @nord roxygen tag to avoid producing Rd files for things we are just experimenting with.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@61303 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 13/12/2011 19:05:37
Showing 1 changed files
NAMESPACE
History View file @ 22b6c34
... ... 
@@ -1,3 +1,5 @@
1 
+importFrom(Rsamtools, path, bamPaths)
2 
+
1 3 
 export(buildGmapDbSNPIndex)
2 4 
 export(buildGmapIITFromFasta)
3 5 
 export(buildGmapIndex)
Browse code

resolved roxygen issue with function having a lowercase equivalent

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@61241 bc3139a8-67e5-0310-9ffc-ced21a209358

Cory Barr authored on 10/12/2011 01:00:07
Showing 1 changed files
NAMESPACE
History View file @ 0d0203a
... ... 
@@ -1,12 +1,3 @@
1 
-importFrom(tools, list_files_with_exts)
2 
-import(BiocGenerics)
3 
-importFrom(IRanges, isSingleString)
4 
-importFrom(Rsamtools, bamPaths, path)
5 
-
6 
-export(GsnapOutput)
7 
-exportClasses(GsnapOutput)
8 
-exportMethods(bamPaths, path)
9 
-
10 1 
 export(buildGmapDbSNPIndex)
11 2 
 export(buildGmapIITFromFasta)
12 3 
 export(buildGmapIndex)
Browse code

update dependencies

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@60633 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 21/11/2011 20:21:53
Showing 1 changed files
NAMESPACE
History View file @ 2296ae7
... ... 
@@ -1,6 +1,7 @@
1 
-importFrom(Rsamtools, bamPaths, path)
2 1 
 importFrom(tools, list_files_with_exts)
2 
+import(BiocGenerics)
3 3 
 importFrom(IRanges, isSingleString)
4 
+importFrom(Rsamtools, bamPaths, path)
4 5
5 6 
 export(GsnapOutput)
6 7 
 exportClasses(GsnapOutput)
Browse code

Add GsnapOutput class, for use with gmapQA

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@58865 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 06/10/2011 20:28:33
Showing 1 changed files
NAMESPACE
History View file @ d3241fa
... ... 
@@ -1,3 +1,11 @@
1 
+importFrom(Rsamtools, bamPaths, path)
2 
+importFrom(tools, list_files_with_exts)
3 
+importFrom(IRanges, isSingleString)
4 
+
5 
+export(GsnapOutput)
6 
+exportClasses(GsnapOutput)
7 
+exportMethods(bamPaths, path)
8 
+
1 9 
 export(buildGmapDbSNPIndex)
2 10 
 export(buildGmapIITFromFasta)
3 11 
 export(buildGmapIndex)
... ... 
@@ -10,4 +18,3 @@ export(getGsnapFileCounts)
10 18 
 export(globals)
11 19 
 export(installGmap)
12 20 
 export(parallelized_gsnap)
13 
-importFrom(IRanges, isSingleString)
Browse code

*alterations to script to install hg19, its splice sites, and dbSNP

*removed obsolete lines in dcf file that globals() reads

*better error checking when creating splice sites and dbSNP IITs

*added a TODO


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@58330 bc3139a8-67e5-0310-9ffc-ced21a209358

Cory Barr authored on 23/09/2011 02:12:38
Showing 1 changed files
NAMESPACE
History View file @ 5de8c9d
... ... 
@@ -2,6 +2,7 @@ export(buildGmapDbSNPIndex)
2 2 
 export(buildGmapIITFromFasta)
3 3 
 export(buildGmapIndex)
4 4 
 export(buildGsnapSNPIIT)
5 
+export(buildRefseqSpliceSites)
5 6 
 export(consolidateGmapFiles)
6 7 
 export(consolidateGsnapFiles)
7 8 
 export(exonsToGmapSpliceSites)
Browse code

*decoupled HTSeqGenieBase from gmapR. Should not have to load HTSeqGenieBase. Might cause problems at present if you do.

*updated script to install pipeline

*fixed bug in buildGmapIndex


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@58273 bc3139a8-67e5-0310-9ffc-ced21a209358

Cory Barr authored on 21/09/2011 11:48:06
Showing 1 changed files
NAMESPACE
History View file @ f746b95
... ... 
@@ -6,5 +6,7 @@ export(consolidateGmapFiles)
6 6 
 export(consolidateGsnapFiles)
7 7 
 export(exonsToGmapSpliceSites)
8 8 
 export(getGsnapFileCounts)
9 
+export(globals)
9 10 
 export(installGmap)
10 11 
 export(parallelized_gsnap)
12 
+importFrom(IRanges, isSingleString)
Browse code

ran roxygen to regenerate collate field in DESCRIPTION

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@58049 bc3139a8-67e5-0310-9ffc-ced21a209358

Cory Barr authored on 15/09/2011 00:36:55
Showing 1 changed files
NAMESPACE
History View file @ 74b2867
... ... 
@@ -1,6 +1,6 @@
1 1 
 export(buildGmapDbSNPIndex)
2 
-export(buildGmapIndex)
3 2 
 export(buildGmapIITFromFasta)
3 
+export(buildGmapIndex)
4 4 
 export(buildGsnapSNPIIT)
5 5 
 export(consolidateGmapFiles)
6 6 
 export(consolidateGsnapFiles)
Browse code

modifications in installGmap

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@58029 bc3139a8-67e5-0310-9ffc-ced21a209358

Cory Barr authored on 14/09/2011 10:06:49
Showing 1 changed files
NAMESPACE
History View file @ cee1c26
... ... 
@@ -1,10 +1,10 @@
1 1 
 export(buildGmapDbSNPIndex)
2 2 
 export(buildGmapIndex)
3 3 
 export(buildGmapIITFromFasta)
4 
-export(installGmap)
5 4 
 export(buildGsnapSNPIIT)
6 5 
 export(consolidateGmapFiles)
7 6 
 export(consolidateGsnapFiles)
8 7 
 export(exonsToGmapSpliceSites)
9 8 
 export(getGsnapFileCounts)
9 
+export(installGmap)
10 10 
 export(parallelized_gsnap)
Browse code

*added test harness for gmapR

*added exonsToGmapSpliceSites and associated unit test


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@57572 bc3139a8-67e5-0310-9ffc-ced21a209358

Cory Barr authored on 20/08/2011 03:36:15
Showing 1 changed files
NAMESPACE
History View file @ e29144b
... ... 
@@ -1,6 +1,10 @@
1 1 
 export(buildGmapDbSNPIndex)
2 2 
 export(buildGmapIndex)
3 
+export(buildGmapIITFromFasta)
3 4 
 export(installGmap)
5 
+export(buildGsnapSNPIIT)
4 6 
 export(consolidateGmapFiles)
7 
+export(consolidateGsnapFiles)
8 
+export(exonsToGmapSpliceSites)
5 9 
 export(getGsnapFileCounts)
6 10 
 export(parallelized_gsnap)
Browse code

add gmapR package

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@57248 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 05/08/2011 07:34:10
Showing 1 changed files
NAMESPACE
History View file @ e92c53c
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,6 @@
1 
+export(buildGmapDbSNPIndex)
2 
+export(buildGmapIndex)
3 
+export(installGmap)
4 
+export(consolidateGmapFiles)
5 
+export(getGsnapFileCounts)
6 
+export(parallelized_gsnap)