Hi,
On 12/14/2014 01:29 PM, Valerie Obenchain wrote:
This should be fixed now (thanks Martin).
We recently deprecated the flag 'isNotPrimaryRead' in favor of
'isNotPrimaryAlignment' (Rsamtools devel).
The new name is actually isSecondaryAlignment.
H.
This affected
GenomicAlignments and others ...
~/b/Rpacks$ grep -lr isNotPrimaryRead *
CoverageView/R/cov.matrix.R
CoverageView/R/cov.interval.R
gage/vignettes/RNA-seqWorkflow.Rnw
hiReadsProcessor/R/hiReadsProcessor.R
QDNAseq/man/binReadCounts.Rd
QDNAseq/R/binReadCounts.R
Rsamtools/NEWS
Rsamtools/man/ScanBamParam-class.Rd
Rsamtools/R/methods-ScanBamParam.R
SplicingGraphs/inst/unitTests/test_countReads-methods.R
SplicingGraphs/inst/scripts/TSPC-utils.R
SplicingGraphs/vignettes/SplicingGraphs.Rnw
SplicingGraphs/man/assignReads.Rd
SplicingGraphs/man/txpath-methods.Rd
systemPipeR/R/utilities.R
These packages should be clear (of this error) on tomorrow's builds.
Thanks.
Val
On 12/14/2014 09:15 AM, Valerie Obenchain wrote:
Hi Sean,
Yes, we are aware of the problem, thanks. Hopefully this will be
resolved for tomorrows builds ... we'll post back when it's fixed.
Val
On 12/14/2014 08:33 AM, Sean Davis wrote:
Hi, Martin, Val, and Herve.
This looks like a little problem with the bitnames in
Rsamtools/GenomicAlignments. Perhaps this is related to some bitnames
being deprecated?
Thanks,
Sean
library(GenomicAlignments)
sbp = ScanBamParam(which=cds[1:100],flag=scanBamFlag(isDuplicate =
FALSE))
x = readGAlignmentPairs(LOCALBAMS[180],param=sbp)
Error in bamFlagAsBitMatrix(flag1, bitnames = "isNotPrimaryRead") :
invalid bitname(s): isNotPrimaryRead
traceback()
8: stop("invalid bitname(s): ", in1string)
7: bamFlagAsBitMatrix(flag1, bitnames = "isNotPrimaryRead")
6: .make_GAlignmentPairs_from_GAlignments(gal, use.mcols = use.mcols)
5: readGAlignmentPairsFromBam(bam, character(), use.names = use.names,
param = param, with.which_label = with.which_label)
4: readGAlignmentPairsFromBam(bam, character(), use.names = use.names,
param = param, with.which_label = with.which_label)
3: readGAlignmentPairsFromBam(file = file, use.names = use.names,
...)
2: readGAlignmentPairsFromBam(file = file, use.names = use.names,
...)
1: readGAlignmentPairs(LOCALBAMS[180], param = sbp)
sessionInfo()
R Under development (unstable) (2014-11-18 r66997)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] C
attached base packages:
[1] stats4 parallel stats graphics grDevices datasets utils
methods base
other attached packages:
[1] TxDb.Hsapiens.UCSC.hg19.knownGene_3.0.0 GenomicFeatures_1.19.7
AnnotationDbi_1.29.11
[4] GenomicAlignments_1.3.14 stringr_0.6.2
plotrix_3.5-10
[7] pd.huex.1.0.st.v2_3.10.0 RSQLite_1.0.0
DBI_0.3.1
[10] limma_3.23.2 oligo_1.31.0
Biobase_2.27.0
[13] oligoClasses_1.29.3 knitr_1.8
VariantAnnotation_1.13.19
[16] Rsamtools_1.19.15 Biostrings_2.35.7
XVector_0.7.3
[19] GenomicRanges_1.19.21 GenomeInfoDb_1.3.7
IRanges_2.1.33
[22] S4Vectors_0.5.14 BiocGenerics_0.13.3
BiocInstaller_1.17.1
loaded via a namespace (and not attached):
[1] BBmisc_1.8 BSgenome_1.35.8 BatchJobs_1.5
BiocParallel_1.1.9 RCurl_1.95-4.5 XML_3.98-1.1
[7] affxparser_1.39.3-1 affyio_1.35.0 base64enc_0.1-2
biomaRt_2.23.5 bit_1.1-12 bitops_1.0-6
[13] brew_1.0-6 checkmate_1.5.1 codetools_0.2-9
digest_0.6.6 evaluate_0.5.5 fail_1.2
[19] ff_2.2-13 foreach_1.4.2 formatR_1.0
htmltools_0.2.6 iterators_1.0.7 knitrBootstrap_1.0.0
[25] markdown_0.7.4 preprocessCore_1.29.0 rmarkdown_0.3.3
rtracklayer_1.27.6 sendmailR_1.2-1 splines_3.2.0
[31] tools_3.2.0 yaml_2.1.13 zlibbioc_1.13.0
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Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
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