From cbfcb4a8e7f4b6528211a30d5d454152ba3cf970 Mon Sep 17 00:00:00 2001 From: Arkadiusz Gladki Date: Sat, 10 Aug 2024 20:33:28 +0200 Subject: [PATCH] bugfix: fix the issue with the custom files not working properly --- DESCRIPTION | 2 +- NEWS.md | 3 +++ R/igvShiny.R | 6 +++--- .../.customGenome-localFiles-sars.R.swp | Bin 12288 -> 0 bytes .../customGenome-localFiles-sars.R | 9 ++++----- 5 files changed, 11 insertions(+), 9 deletions(-) delete mode 100644 inst/demos/customGenomes/.customGenome-localFiles-sars.R.swp diff --git a/DESCRIPTION b/DESCRIPTION index cfb0d79..2ceb463 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: igvShiny Title: igvShiny: a wrapper of Integrative Genomics Viewer (IGV - an interactive tool for visualization and exploration integrated genomic data) -Version: 1.0.0 +Version: 1.0.1 Date: 2024-08-10 Authors@R: c( person("Paul","Shannon", role = c("aut"), diff --git a/NEWS.md b/NEWS.md index fb3bbe7..16575c2 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,6 @@ +## igvShiny 1.0.1 - 2024-08-10 +* fix issue with custom files not working properly + ## igvShiny 1.0.0 - 2024-08-10 * sync with Bioconductor (3_19 release) diff --git a/R/igvShiny.R b/R/igvShiny.R index ca5aae7..5ffe1b2 100644 --- a/R/igvShiny.R +++ b/R/igvShiny.R @@ -84,13 +84,13 @@ igvShiny <- function(genomeOptions, destination <- file.path(directory.name, basename(gff3.file)) file.copy(gff3.file, destination, overwrite = TRUE) genomeOptions[["annotation"]] <- - file.path(directory.name, basename(gff3.file)) + file.path(basename(directory.name), basename(gff3.file)) } # now that they have been copied, store the new paths genomeOptions[["fasta"]] <- - file.path(directory.name, basename(fasta.file)) + file.path(basename(directory.name), basename(fasta.file)) genomeOptions[["fastaIndex"]] <- - file.path(directory.name, basename(fasta.indexFile)) + file.path(basename(directory.name), basename(fasta.indexFile)) } # if custom genome, local files state[["requestedHeight"]] <- height diff --git a/inst/demos/customGenomes/.customGenome-localFiles-sars.R.swp b/inst/demos/customGenomes/.customGenome-localFiles-sars.R.swp deleted file mode 100644 index 2eab7bdc289e9f875d14eca4dfc5182c31f27316..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 12288 zcmeHNPjBQj6n8-a7Fa-VgNvIkG?8X9?NpRjFozMlr2{SPcGPlMmdcYj8E+FivYly1 zrEuT_AdcKQB2Gwq;{$Nw8^DDRfK&+(7oPK{qp4a1D>M?wQGbnN`#rz+d(XD2zQNK# zZyT@sO9-A95IX%m4_>~p{P=@+=TMxG@Q4vJ@|RCFueraueS3BL`l+8(6I(IUtvHlf zLUbf#+G6pjKV*E|VqED~NK>I&L9Vn&-=SQjbo#5Ah=3#;ETO8Yh*bXG^-J0j%YbFz zf`OZ8rM+Bi^#x}hzx3k%#fWWK1}p=X0n318z%pPNunbrRECc_426Q%uJ_R=)t6XhW z@3~9w>eId~1C{~HfMvikU>UFsSOzQumI2FvWxz6E8Tbz}KthB*egdK0C&765|9}1W z|1ZxY^dsPVz(c@Y!1;3seGb?Hv;nUGe!Yp%7k~}G`LhUp3FrYf0d2tfGYEYP$N_D@ z`O^q}4fqJ~+YN+%0(=K}2)GM)6>tmi$5ROX0Qd&*8Gr*00UrPk0Pg{Q2AjVEi~%WN zA7K300ocbfU>UFsSOzQuvt$5ce1_ncGWBfTEOT?#z>3Ndm7eK8!!%J8pPIJJxtVd* z)CSIk)ScC})i*rEA~%*aOI&A2;)toC)4=_)@)?hW>)pHOa1l~YQtI5l@8Q?*JmZ>5 z5@ykk?E-D0fGR*{6)r^2>*8!KY(nM;;V=#e-RQ9Sm!w+i#*MX!N!24)u-w%>E3Bxm6+iK#n7GmWW#=P3i(fDIPQ>(rXNAE=aq?at>TD4 z?0XROlg^}B=&5q#TFL2wLbz1%2+|?Zq)g&T&1#*-)9YOO1y!)YQCSAt+30Td@BB0S z8E2Z2WJ^FjZO0)=0?SWr8I$oDRMFBd4-ZJfz+_r3*UxBBZLjy?aOr5K6WTz<%Sbu> z?q0w7wm4|E9fU4L%SSn)6rqr1e>no z)LRqIZ-<^}BW0SVh`FR3RL$o6AYr&imB?j4cTIpC4fn;7GS*Zrv)v$Kejq7i#KnZ- zHkvmB^n@v`CIetP4hS!=0Gww<_!T~;_*gPcu^v)M8#qriOF?5Y#sQqzc}hb(7@PCl zf1p5xq%mxMEFxUoVpM4#8zmslF^DDQX@(Z!Ef{^A!oma>`*NZIYf+hNl2>6!Vj;m2I81l|))PDmqQWyUG?P?OUfeGP7n_O& oGm75=PS`*aId%t3q-0NfsO}i*G&yErOtqSH)|ofyDH!t5pW(cy$^ZZW diff --git a/inst/demos/customGenomes/customGenome-localFiles-sars.R b/inst/demos/customGenomes/customGenome-localFiles-sars.R index 7d1fedb..821a551 100644 --- a/inst/demos/customGenomes/customGenome-localFiles-sars.R +++ b/inst/demos/customGenomes/customGenome-localFiles-sars.R @@ -11,12 +11,13 @@ annotation.file <- file.path(data.directory, "Sars_cov_2.ASM985889v3.101.gff3") title <- "SARS-CoV-2" genomeOptions <- parseAndValidateGenomeSpec(genomeName=title, - initialLocus="all", + initialLocus= NA, stockGenome=FALSE, dataMode="localFiles", fasta=fasta.file, fastaIndex=fastaIndex.file, - genomeAnnotation=annotation.file) + genomeAnnotation=annotation.file + ) #---------------------------------------------------------------------------------------------------- ui = shinyUI(fluidPage( igvShinyOutput('igvShiny_0'), @@ -26,9 +27,7 @@ server = function(input, output, session) { output$igvShiny_0 <- renderIgvShiny({ cat("--- starting renderIgvShiny\n"); - x <- igvShiny(genomeOptions, - displayMode="SQUISHED", - ) + x <- igvShiny(genomeOptions, displayMode="SQUISHED") return(x) })