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Revision: 76730
Author: mtmorgan
Date: Sun, 19 May 2013 12:13:41 GMT
Paths:
Modified  /trunk/madman/Rpacks/ShortRead/R/SnapshotFunction-helpers.R
Modified  /trunk/madman/Rpacks/ShortRead/R/Snapshot.R
Modified  /trunk/madman/Rpacks/ShortRead/R/spViewPerFeature.R
Modified  /trunk/madman/Rpacks/ShortRead/man/Snapshot-class.Rd
quieten warnings from Snapshot

- use seqlevels<-
- avoid setting scales in update() -- bug in lattice??
Revision: 76728
Author: mtmorgan
Date: Sun, 19 May 2013 04:01:52 GMT
Paths:
Modified  /trunk/madman/Rpacks/ShortRead/DESCRIPTION
Modified  /trunk/madman/Rpacks/ShortRead/NEWS
DESCRIPTION and NEWS update
Revision: 76727
Author: mtmorgan
Date: Sun, 19 May 2013 02:36:24 GMT
Paths:
Modified  /trunk/madman/Rpacks/ShortRead/inst/unitTests/test_trimEnds.R
Added  /trunk/madman/Rpacks/ShortRead/R/trimEnds.R
Modified  /trunk/madman/Rpacks/ShortRead/inst/unitTests/test_trimTails.R
Modified  /trunk/madman/Rpacks/ShortRead/man/trimTails.Rd
trim*,character-methods using filterFastq
Revision: 76726
Author: mtmorgan
Date: Sun, 19 May 2013 02:35:41 GMT
Paths:
Added  /trunk/madman/Rpacks/ShortRead/inst/unitTests/test_filterFastq.R
Added  /trunk/madman/Rpacks/ShortRead/man/filterFastq.Rd
Added  /trunk/madman/Rpacks/ShortRead/R/filterFastq.R
filterFastq methods
Revision: 76725
Author: mtmorgan
Date: Sat, 18 May 2013 19:19:18 GMT
Paths:
Modified  /trunk/madman/Rpacks/ShortRead/inst/unitTests/test_writeFastq_test.R
Modified  /trunk/madman/Rpacks/ShortRead/R/methods-ShortReadQ.R
write 0-length fastq files
Revision: 76724
Author: mtmorgan
Date: Sat, 18 May 2013 19:16:25 GMT
Paths:
Modified  /trunk/madman/Rpacks/ShortRead/DESCRIPTION
Modified  /trunk/madman/Rpacks/ShortRead/R/methods-QualityScore.R
Modified  /trunk/madman/Rpacks/ShortRead/man/QualityScore-class.Rd
Modified  /trunk/madman/Rpacks/ShortRead/NAMESPACE
encoding,QualityScore-methods
Revision: 76723
Author: mtmorgan
Date: Sat, 18 May 2013 19:06:16 GMT
Paths:
Modified  /trunk/madman/Rpacks/Biostrings/R/XStringQuality-class.R
Modified  /trunk/madman/Rpacks/Biostrings/NAMESPACE
Modified  /trunk/madman/Rpacks/Biostrings/DESCRIPTION
Modified  /trunk/madman/Rpacks/Biostrings/man/XStringQuality-class.Rd
alphabet and encoding methods for XStringQuality
Revision: 76722
Author: hpages
Date: Sat, 18 May 2013 04:56:45 GMT
Paths:
Modified  /trunk/madman/Rpacks/SplicingGraphs/inst/doc/SplicingGraphs.Rnw
small tweaks to vignette
Revision: 76721
Author: radivot
Date: Sat, 18 May 2013 03:09:57 GMT
Paths:
Modified  /trunk/madman/Rpacks/SBMLR/R/simulate.r
Modified  /trunk/madman/Rpacks/SBMLR/R/readSBML.r
Modified  /trunk/madman/Rpacks/SBMLR/R/summary.SBML.r
Modified  /trunk/madman/Rpacks/SBMLR/R/saveSBML.r
got it to pass check with VV additions
Revision: 76720
Author: hpages
Date: Sat, 18 May 2013 02:01:51 GMT
Paths:
Added  /trunk/madman/Rpacks/SplicingGraphs/inst/doc/precomputed_results/sg_with_bubbles.rda
Modified  /trunk/madman/Rpacks/SplicingGraphs/inst/doc/precomputed_results/sg_with_reads.rda
Modified  /trunk/madman/Rpacks/SplicingGraphs/DESCRIPTION
Modified  /trunk/madman/Rpacks/SplicingGraphs/inst/doc/SplicingGraphs.Rnw
Modified  /trunk/madman/Rpacks/SplicingGraphs/TODO
Deleted  /trunk/madman/Rpacks/SplicingGraphs/inst/doc/precomputed_results/sg.rda
Use new RNAseqData.HeLa.bam.chr14 dataset in the vignette instead of
TBX20BamSubset.
Revision: 76719
Author: y.liao
Date: Fri, 17 May 2013 23:53:47 GMT
Paths:
Modified  /trunk/madman/Rpacks/Rsubread/src/readSummary.c
minor updated
Revision: 76718
Author: y.liao
Date: Fri, 17 May 2013 23:53:21 GMT
Paths:
Modified  /trunk/madman/Rpacks/Rsubread/src/readSummary.c
minor updated
Revision: 76717
Author: y.liao
Date: Fri, 17 May 2013 23:46:03 GMT
Paths:
Modified  /trunk/madman/Rpacks/Rsubread/src/readSummary.c
minor updated
Revision: 76716
Author: radivot
Date: Fri, 17 May 2013 23:33:29 GMT
Paths:
Modified  /trunk/madman/Rpacks/SBMLR/R/saveSBMLR.r
Modified  /trunk/madman/Rpacks/SBMLR/R/simulate.r
Modified  /trunk/madman/Rpacks/SBMLR/R/readSBML.r
Modified  /trunk/madman/Rpacks/SBMLR/R/readSBMLR.r
Modified  /trunk/madman/Rpacks/SBMLR/R/saveSBML.r
Added in the rest of VV's changes, i.e. from SBMLR on github
Revision: 76715
Author: l.chavez
Date: Fri, 17 May 2013 21:55:54 GMT
Paths:
Modified  /trunk/madman/Rpacks/MEDIPS/R/MEDIPS.mergeFrames.R
Modified  /trunk/madman/Rpacks/MEDIPS/DESCRIPTION
MEDIPS.mergeFrames trim parameter
Revision: 76714
Author: p.haverty
Date: Fri, 17 May 2013 20:21:10 GMT
Paths:
Deleted  /trunk/madman/Rpacks/genoset/man/rangeSegMeanLength.Rd
Modified  /trunk/madman/Rpacks/genoset/man/rangeSegMeanLength-methods.Rd
Modified  /trunk/madman/Rpacks/genoset/inst/unitTests/test_segments.R
Modified  /trunk/madman/Rpacks/genoset/R/segments.R
Modified  /trunk/madman/Rpacks/genoset/R/genoset-class.R
Updated tests for rangeSegMeanLength and Rd
Revision: 76713
Author: m.lawrence
Date: Fri, 17 May 2013 17:46:48 GMT
Paths:
Modified  /trunk/madman/Rpacks/ggbio/R/plotRangesLinkedToData.R
plotRangesLinkedToData now a generic, with a method for
SummarizedExperiment. Not tested at all.
Revision: 76703
Author: v.obenchain
Date: Fri, 17 May 2013 15:50:58 GMT
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/R/utils.R
Clean up how the default value is set for 'showHeaderLines' and 'showTailLine'.
Revision: 76702
Author: radivot
Date: Fri, 17 May 2013 15:02:04 GMT
Paths:
Modified  /trunk/madman/Rpacks/SBMLR
svn ignore RStudio project file added
Revision: 76701
Author: radivot
Date: Fri, 17 May 2013 15:01:03 GMT
Paths:
Modified  /trunk/madman/Rpacks/SBMLR/inst/doc/quick-start.Rnw
Modified  /trunk/madman/Rpacks/SBMLR
Modified  /trunk/madman/Rpacks/SBMLR/man/simulate.Rd
Modified  /trunk/madman/Rpacks/SBMLR/DESCRIPTION
Modified  /trunk/madman/Rpacks/SBMLR/R/simulate.r
Modified  /trunk/madman/Rpacks/SBMLR/R/summary.SBML.r
Added  /trunk/madman/Rpacks/SBMLR/NEWS
 Vishak Venkateswaran has a branch of SBMLR up at github that I'm starting to go through. So far I added his changes to summary and simulate.
Revision: 76700
Author: m.stadler
Date: Fri, 17 May 2013 13:58:27 GMT
Paths:
Modified  /trunk/madman/Rpacks/QuasR/man/qAlign.Rd
update qAlign documentation with index storage locations
Revision: 76697
Author: r.day
Date: Fri, 17 May 2013 02:45:19 GMT
Paths:
Modified  /trunk/madman/Rpacks/IdMappingAnalysis/R/expectedUtility.R
expectedUtility:
 added guarantee parameter,
 corrected the format of the "details" block,
 put quotes around "piHat".
Revision: 76696
Author: r.day
Date: Fri, 17 May 2013 02:41:27 GMT
Paths:
Modified  /trunk/madman/Rpacks/IdMappingAnalysis/R/fit2clusters.R
Corrected Vstart -> VStart
Added Ysigsq as @param
Removed references to global variables.
Removed test code outside of function.
Revision: 76695
Author: r.day
Date: Fri, 17 May 2013 02:39:42 GMT
Paths:
Modified  /trunk/madman/Rpacks/IdMappingAnalysis/man/expectedUtility.Rd
Corrected Vstart -> VStart
Added Ysigsq as @param
Removed references to global variables.
Removed test code outside of function.
Revision: 76694
Author: r.day
Date: Fri, 17 May 2013 02:38:23 GMT
Paths:
Modified  /trunk/madman/Rpacks/IdMappingAnalysis/man/fit2clusters.Rd
Corrected Vstart -> VStart
Added Ysigsq as @param
Removed references to global variables.
Removed test code outside of function.
Revision: 76693
Author: r.day
Date: Fri, 17 May 2013 02:25:35 GMT
Paths:
Modified  /trunk/madman/Rpacks/IdMappingAnalysis/R/zzz.R
Replacing .First.lib by .onLoad
Revision: 76692
Author: y.liao
Date: Fri, 17 May 2013 00:00:00 GMT
Paths:
Modified  /trunk/madman/Rpacks/Rsubread/src/readSummary.c
robust featureCount load_features
Revision: 76691
Author: y.liao
Date: Fri, 17 May 2013 00:00:00 GMT
Paths:
Modified  /trunk/madman/Rpacks/Rsubread/src/readSummary.c
robust featureCount load_features
Revision: 76690
Author: hpages
Date: Fri, 17 May 2013 00:00:00 GMT
Paths:
Modified  /trunk/madman/Rpacks/SplicingGraphs/DESCRIPTION
Modified  /trunk/madman/Rpacks/SplicingGraphs/man/plotTranscripts-methods.Rd
Modified  /trunk/madman/Rpacks/SplicingGraphs/R/plotTranscripts-methods.R
Add 'max.plot.reads' arg to plotTranscripts(). Default is 200.
Revision: 76689
Author: v.obenchain
Date: Thu, 16 May 2013 23:01:42 GMT
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/R/utils.R
Fix bug in 'show' related to 'showHeaderLines' and 'showTailLines'.
Revision: 76684
Author: v.obenchain
Date: Thu, 16 May 2013 22:04:22 GMT
Paths:
Modified  /trunk/madman/Rpacks/ensemblVEP/R/methods-parseCSQToGRanges.R
Modified  /trunk/madman/Rpacks/ensemblVEP/DESCRIPTION
Modified  /trunk/madman/Rpacks/ensemblVEP/inst/doc/ensemblVEP.Rnw
Modified  /trunk/madman/Rpacks/ensemblVEP/man/parseCSQToGRanges.Rd
Modify 'VCFRowID' argument to parseCSQToGRanges() to handle results returned in
any order or subset.
Revision: 76679
Author: mtmorgan
Date: Thu, 16 May 2013 21:12:43 GMT
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/DESCRIPTION
Modified  /trunk/madman/Rpacks/GenomicRanges/R/SummarizedExperiment-class.R
more efficient ref class constructor

- new empty instance, the update slots
Revision: 76678
Author: v.obenchain
Date: Thu, 16 May 2013 20:27:51 GMT
Paths:
Modified  /trunk/madman/Rpacks/VariantAnnotation/man/predictCoding-methods.Rd
Modified  /trunk/madman/Rpacks/VariantAnnotation/inst/unitTests/test_VCF-class.R
Modified  /trunk/madman/Rpacks/VariantAnnotation/man/locateVariants-methods.Rd
Modified  /trunk/madman/Rpacks/VariantAnnotation/man/VCF-class.Rd
Modified  /trunk/madman/Rpacks/VariantAnnotation/DESCRIPTION
Modified  /trunk/madman/Rpacks/VariantAnnotation/man/summarizeVariants-methods.Rd
Modified  /trunk/madman/Rpacks/VariantAnnotation/R/methods-scanVcf.R
Modified  /trunk/madman/Rpacks/VariantAnnotation/man/getTranscriptSeqs-methods.Rd
Modified  /trunk/madman/Rpacks/VariantAnnotation/inst/doc/VariantAnnotation.Rnw
- Replace calls to keepSeqlevels() and renameSeqlevels() with seqlevels().
- Header info is accessed twice in readVcf() which resulted in a double
  (identical) warning if one was thrown. Now only a single warning is thrown.
Revision: 76677
Author: v.obenchain
Date: Thu, 16 May 2013 19:14:40 GMT
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/man/seqinfo.Rd
Modified  /trunk/madman/Rpacks/GenomicRanges/inst/unitTests/test_Seqinfo-class.R
Work on examples on 'seqinfo' man page and 'Seqinfo' unit tests.
Revision: 76665
Author: v.obenchain
Date: Thu, 16 May 2013 16:06:26 GMT
Paths:
Modified  /trunk/madman/Rpacks/GenomicRanges/man/seqlevels-utils.Rd
Modified  /trunk/madman/Rpacks/GenomicRanges/man/seqinfo.Rd
Add author to seqinfo man page; \seealso on deprecated seqlevels-utils
page now points to the seqinfo page.
Revision: 76656
Author: d.gaidatzis
Date: Thu, 16 May 2013 15:26:28 GMT
Paths:
Modified  /trunk/madman/Rpacks/QuasR/DESCRIPTION
Modified  /trunk/madman/Rpacks/QuasR/R/createAlignments-functions.R
Fixed bug when adding aux alignments to preexisting aux alignments
Revision: 76651
Author: w.ligtenberg
Date: Thu, 16 May 2013 13:52:23 GMT
Paths:
Modified  /trunk/madman/Rpacks/MLP/R/addGeneSetDescription.R
Modified  /trunk/madman/Rpacks/MLP/DESCRIPTION
fixed bug caused by changes in reactome.db: reactome_db --> DB_ID
Revision: 76650
Author: s.piccolo
Date: Thu, 16 May 2013 02:07:35 GMT
Paths:
Modified  /trunk/madman/Rpacks/SCAN.UPC/DESCRIPTION
Increased version
Revision: 76649
Author: m.lawrence
Date: Thu, 16 May 2013 00:00:00 GMT
Paths:
Modified  /trunk/madman/Rpacks/gmapR/R/makeGmapGenomePackage.R
Modified  /trunk/madman/Rpacks/gmapR/inst/GmapGenomePackage-template/R/zzz.R
Modified  /trunk/madman/Rpacks/gmapR/DESCRIPTION
package created by makeGmapGenomePackage now have a GmapGenome with
the correct name
Revision: 76647
Author: mtmorgan
Date: Thu, 16 May 2013 00:00:00 GMT
Paths:
Modified  /trunk/madman/Rpacks/Rsamtools/R/methods-BamFile.R
Modified  /trunk/madman/Rpacks/Rsamtools/DESCRIPTION
efficient filterBam when no filter callbacks provided
Revision: 76644
Author: mtmorgan
Date: Thu, 16 May 2013 00:00:00 GMT
Paths:
Modified  /trunk/madman/Rpacks/Rsamtools/src/io_sam.c
Modified  /trunk/madman/Rpacks/Rsamtools/src/bambuffer.c
Modified  /trunk/madman/Rpacks/Rsamtools/src/bamfile.c
white space
Revision: 76635
Author: v.obenchain
Date: Wed, 15 May 2013 23:21:56 GMT
Paths:
Deleted  /trunk/madman/Rpacks/GenomicRanges/inst/unitTests/test_seqlevels-utils.R
Modified  /trunk/madman/Rpacks/GenomicRanges/man/seqinfo.Rd
Modified  /trunk/madman/Rpacks/GenomicRanges/inst/unitTests/test_Seqinfo-class.R
Moved unit tests for keepSeqlevels() and renameSeqlevels() to
test_Seqinfo-class.R; removed test_Seqinfo-class.R.
Revision: 76633
Author: l.gatto
Date: Wed, 15 May 2013 00:00:00 GMT
Paths:
Modified  /trunk/madman/Rpacks/MSnbase/NEWS
Modified  /trunk/madman/Rpacks/MSnbase/DESCRIPTION
Merge branch 'master' into local-hedgehog
Revision: 76632
Author: mtmorgan
Date: Wed, 15 May 2013 22:41:30 GMT
Paths:
Modified  /trunk/madman/Rpacks/Rsamtools/R/methods-BcfFile.R
Modified  /trunk/madman/Rpacks/Rsamtools/DESCRIPTION
de-duplicate B/VCF header lines

- avoids error message about duplicate keys

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