Hi,

I am trying to use rtracklayer's import.chain function to load a chain file from UCSC. However, I get a weird error. Below is a reproducible example and the error I get. What is happening here?

library(rtracklayer)

download.file("http://hgdownload.cse.ucsc.edu/goldenpath/hg19/vsSelf/hg19.hg19.all.chain.gz",
              "hg19.hg19.all.chain.gz")

system("gzip -d hg19.hg19.all.chain.gz")

chain <- import.chain("hg19.hg19.all.chain")

The error is:

Error in .local(con, format, text, ...) : expected 11 elements in header, got 3, on line 1

What is import looking for here? My sessionInfo() is below.

R version 3.3.0 (2016-05-03) Platform: x86_64-redhat-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

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=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base other attached packages: [1] rtracklayer_1.32.2 AnnotationHub_2.4.2 [3] InteractionSet_1.0.4 SummarizedExperiment_1.2.3 [5] Biobase_2.32.0 GenomicRanges_1.24.3 [7] GenomeInfoDb_1.8.7 IRanges_2.6.1 [9] S4Vectors_0.10.3 BiocGenerics_0.18.0 [11] Chicago_1.0.4 data.table_1.10.4-3 [13] magrittr_1.5 scales_0.5.0.9000

loaded via a namespace (and not attached): [1] Rcpp_0.12.14 lattice_0.20-33 [3] Delaporte_6.2.0 Rsamtools_1.24.0 [5] Biostrings_2.40.2 digest_0.6.12 [7] mime_0.5 R6_2.2.2 [9] plyr_1.8.4 backports_1.1.2 [11] acepack_1.4.1 RSQLite_1.0.0 [13] httr_1.3.1 ggplot2_2.2.1.9000 [15] BiocInstaller_1.22.3 zlibbioc_1.18.0 [17] rlang_0.1.4 lazyeval_0.2.1 [19] curl_3.0 rstudioapi_0.6 [21] rpart_4.1-10 Matrix_1.2-6 [23] checkmate_1.8.5 splines_3.3.0 [25] BiocParallel_1.6.6 stringr_1.2.0 [27] foreign_0.8-66 htmlwidgets_0.9 [29] RCurl_1.95-4.8 munsell_0.4.3 [31] shiny_1.0.3 compiler_3.3.0 [33] httpuv_1.3.5 base64enc_0.1-3 [35] htmltools_0.3.6 nnet_7.3-12 [37] tibble_1.3.4 gridExtra_2.3 [39] htmlTable_1.12 interactiveDisplayBase_1.10.3 [41] Hmisc_4.1-1 matrixStats_0.54.0 [43] XML_3.98-1.4 GenomicAlignments_1.8.4 [45] bitops_1.0-6 MASS_7.3-45 [47] grid_3.3.0 xtable_1.8-2 [49] gtable_0.2.0 DBI_0.5 [51] stringi_1.1.6 XVector_0.12.1 [53] latticeExtra_0.6-28 Formula_1.2-3 [55] RColorBrewer_1.1-2 tools_3.3.0 [57] survival_2.42-6 AnnotationDbi_1.34.4 [59] colorspace_1.2-6 cluster_2.0.4 [61] knitr_1.14

Looks like the UCSC chain file format has changed, or at least they are using features that they weren't before. It may take a bit for me to fix the parser.