GAlignments GappedAlignments issue

[joe-nas]

Hi Tengfei,

I think the methods to handle GappedAlignments in bioconductor 2.12 need to be changed in work with GAlignments.

regards, Jonas

sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-pc-linux-gnu (64-bit)

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] parallel stats graphics grDevices utils datasets methods
[8] base

other attached packages: [1] Rsamtools_1.13.8 Biostrings_2.29.1 rtracklayer_1.20.2
[4] ggbio_1.8.3 ggplot2_0.9.3.1 GenomicFeatures_1.13.1 [7] AnnotationDbi_1.23.5 Biobase_2.21.0 GenomicRanges_1.13.8
[10] IRanges_1.19.3 BiocGenerics_0.7.2

loaded via a namespace (and not attached): [1] biomaRt_2.17.0 biovizBase_1.9.1 bitops_1.0-5
[4] BSgenome_1.29.0 cluster_1.14.4 colorspace_1.2-2
[7] DBI_0.2-7 dichromat_2.0-0 digest_0.6.3
[10] grid_3.0.1 gridExtra_0.9.1 gtable_0.1.2
[13] Hmisc_3.10-1.1 labeling_0.1 lattice_0.20-15
[16] MASS_7.3-26 munsell_0.4 plyr_1.8
[19] proto_0.3-10 RColorBrewer_1.0-5 RCurl_1.95-4.1
[22] reshape2_1.2.2 RSQLite_0.11.4 scales_0.2.3
[25] stats4_3.0.1 stringr_0.6.2 tools_3.0.1
[28] VariantAnnotation_1.7.16 XML_3.96-1.1 zlibbioc_1.7.0

[tengfei]

Hi Jonas,

Thanks, I think this was fixed in devel branch.

Tengfei

On Tue, Jun 4, 2013 at 4:49 AM, joe-nas [email protected] wrote:

Hi Tengfei,

I think the methods to handle GappedAlignments in bioconductor 2.12 need to be changed in work with GAlignments.

regards, Jonas

sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-pc-linux-gnu (64-bit)

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C

[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8

[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8

[7] LC_PAPER=C LC_NAME=C

[9] LC_ADDRESS=C LC_TELEPHONE=C

[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] parallel stats graphics grDevices utils datasets methods

[8] base

other attached packages: [1] Rsamtools_1.13.8 Biostrings_2.29.1 rtracklayer_1.20.2

[4] ggbio_1.8.3 ggplot2_0.9.3.1 GenomicFeatures_1.13.1 [7] AnnotationDbi_1.23.5 Biobase_2.21.0 GenomicRanges_1.13.8

[10] IRanges_1.19.3 BiocGenerics_0.7.2

loaded via a namespace (and not attached): [1] biomaRt_2.17.0 biovizBase_1.9.1 bitops_1.0-5

[4] BSgenome_1.29.0 cluster_1.14.4 colorspace_1.2-2

[7] DBI_0.2-7 dichromat_2.0-0 digest_0.6.3

[10] grid_3.0.1 gridExtra_0.9.1 gtable_0.1.2

[13] Hmisc_3.10-1.1 labeling_0.1 lattice_0.20-15

[16] MASS_7.3-26 munsell_0.4 plyr_1.8

[19] proto_0.3-10 RColorBrewer_1.0-5 RCurl_1.95-4.1

[22] reshape2_1.2.2 RSQLite_0.11.4 scales_0.2.3

[25] stats4_3.0.1 stringr_0.6.2 tools_3.0.1

[28] VariantAnnotation_1.7.16 XML_3.96-1.1 zlibbioc_1.7.0

— Reply to this email directly or view it on GitHubhttps://github.com/tengfei/ggbio/issues/37 .

Tengfei Yin MCDB PhD student 1620 Howe Hall, 2274, Iowa State University Ames, IA,50011-2274