--- /srv/rebuilderd/tmp/rebuilderdbGAzJN/inputs/r-bioc-structuralvariantannotation_1.28.0+ds-1_all.deb +++ /srv/rebuilderd/tmp/rebuilderdbGAzJN/out/r-bioc-structuralvariantannotation_1.28.0+ds-1_all.deb ├── file list │ @@ -1,3 +1,3 @@ │ -rw-r--r-- 0 0 0 4 2026-08-12 10:54:19.000000 debian-binary │ --rw-r--r-- 0 0 0 2508 2026-08-12 10:54:19.000000 control.tar.xz │ --rw-r--r-- 0 0 0 397996 2026-08-12 10:54:19.000000 data.tar.xz │ +-rw-r--r-- 0 0 0 2408 2026-08-12 10:54:19.000000 control.tar.xz │ +-rw-r--r-- 0 0 0 398384 2026-08-12 10:54:19.000000 data.tar.xz ├── control.tar.xz │ ├── control.tar │ │ ├── file list │ │ │ @@ -1,3 +1,3 @@ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 10:54:19.000000 ./ │ │ │ --rw-r--r-- 0 root (0) root (0) 1193 2026-08-12 10:54:19.000000 ./control │ │ │ --rw-r--r-- 0 root (0) root (0) 6085 2026-08-12 10:54:19.000000 ./md5sums │ │ │ +-rw-r--r-- 0 root (0) root (0) 1023 2026-08-12 10:54:19.000000 ./control │ │ │ +-rw-r--r-- 0 root (0) root (0) 5982 2026-08-12 10:54:19.000000 ./md5sums │ │ ├── ./control │ │ │ @@ -1,14 +1,13 @@ │ │ │ Package: r-bioc-structuralvariantannotation │ │ │ Version: 1.28.0+ds-1 │ │ │ Architecture: all │ │ │ Maintainer: Debian R Packages Maintainers │ │ │ -Installed-Size: 1299 │ │ │ +Installed-Size: 1298 │ │ │ Depends: r-api-4.0, r-api-bioc-3.23, r-bioc-genomicranges, r-bioc-rtracklayer, r-bioc-variantannotation, r-bioc-biocgenerics, r-cran-assertthat, r-bioc-biostrings, r-bioc-pwalign, r-cran-stringr, r-cran-dplyr, r-cran-rlang, r-bioc-genomicfeatures, r-bioc-iranges, r-bioc-s4vectors, r-bioc-summarizedexperiment, r-bioc-genomeinfodb, r-pkg-team-core-architecture │ │ │ -Suggests: r-cran-ggplot2, r-cran-devtools, r-cran-testthat (>= 2.1.0), r-cran-roxygen2, r-cran-rmarkdown, r-cran-tidyverse, r-cran-knitr, r-bioc-ggbio, r-bioc-biovizbase │ │ │ Section: gnu-r │ │ │ Priority: optional │ │ │ Homepage: https://bioconductor.org/packages/StructuralVariantAnnotation/ │ │ │ Description: Variant annotations for structural variants │ │ │ StructuralVariantAnnotation contains useful helper │ │ │ functions for dealing with structural variants in VCF format. │ │ │ The packages contains functions for parsing VCFs from a number │ │ ├── ./md5sums │ │ │ ├── ./md5sums │ │ │ │┄ Files differ │ │ │ ├── line order │ │ │ │ @@ -2,15 +2,14 @@ │ │ │ │ usr/lib/R/site-library/StructuralVariantAnnotation/INDEX │ │ │ │ usr/lib/R/site-library/StructuralVariantAnnotation/Meta/Rd.rds │ │ │ │ usr/lib/R/site-library/StructuralVariantAnnotation/Meta/features.rds │ │ │ │ usr/lib/R/site-library/StructuralVariantAnnotation/Meta/hsearch.rds │ │ │ │ usr/lib/R/site-library/StructuralVariantAnnotation/Meta/links.rds │ │ │ │ usr/lib/R/site-library/StructuralVariantAnnotation/Meta/nsInfo.rds │ │ │ │ usr/lib/R/site-library/StructuralVariantAnnotation/Meta/package.rds │ │ │ │ -usr/lib/R/site-library/StructuralVariantAnnotation/Meta/vignette.rds │ │ │ │ usr/lib/R/site-library/StructuralVariantAnnotation/NAMESPACE │ │ │ │ usr/lib/R/site-library/StructuralVariantAnnotation/NEWS │ │ │ │ usr/lib/R/site-library/StructuralVariantAnnotation/R/StructuralVariantAnnotation │ │ │ │ usr/lib/R/site-library/StructuralVariantAnnotation/R/StructuralVariantAnnotation.rdb │ │ │ │ usr/lib/R/site-library/StructuralVariantAnnotation/R/StructuralVariantAnnotation.rdx │ │ │ │ usr/lib/R/site-library/StructuralVariantAnnotation/README.md │ │ │ │ usr/lib/R/site-library/StructuralVariantAnnotation/doc/index.html ├── data.tar.xz │ ├── data.tar │ │ ├── file list │ │ │ @@ -9,24 +9,23 @@ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 10:54:19.000000 ./usr/lib/R/site-library/StructuralVariantAnnotation/Meta/ │ │ │ -rw-r--r-- 0 root (0) root (0) 1594 2026-08-12 10:54:19.000000 ./usr/lib/R/site-library/StructuralVariantAnnotation/Meta/Rd.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 123 2026-08-12 10:54:19.000000 ./usr/lib/R/site-library/StructuralVariantAnnotation/Meta/features.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 1535 2026-08-12 10:54:19.000000 ./usr/lib/R/site-library/StructuralVariantAnnotation/Meta/hsearch.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 590 2026-08-12 10:54:19.000000 ./usr/lib/R/site-library/StructuralVariantAnnotation/Meta/links.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 656 2026-08-12 10:54:19.000000 ./usr/lib/R/site-library/StructuralVariantAnnotation/Meta/nsInfo.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 1674 2026-08-12 10:54:19.000000 ./usr/lib/R/site-library/StructuralVariantAnnotation/Meta/package.rds │ │ │ --rw-r--r-- 0 root (0) root (0) 224 2026-08-12 10:54:19.000000 ./usr/lib/R/site-library/StructuralVariantAnnotation/Meta/vignette.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 1269 2026-08-12 10:54:19.000000 ./usr/lib/R/site-library/StructuralVariantAnnotation/NAMESPACE │ │ │ -rw-r--r-- 0 root (0) root (0) 67 2026-08-12 10:54:19.000000 ./usr/lib/R/site-library/StructuralVariantAnnotation/NEWS │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 10:54:19.000000 ./usr/lib/R/site-library/StructuralVariantAnnotation/R/ │ │ │ -rw-r--r-- 0 root (0) root (0) 1058 2026-08-12 10:54:19.000000 ./usr/lib/R/site-library/StructuralVariantAnnotation/R/StructuralVariantAnnotation │ │ │ --rw-r--r-- 0 root (0) root (0) 130225 2026-08-12 10:54:19.000000 ./usr/lib/R/site-library/StructuralVariantAnnotation/R/StructuralVariantAnnotation.rdb │ │ │ --rw-r--r-- 0 root (0) root (0) 1529 2026-08-12 10:54:19.000000 ./usr/lib/R/site-library/StructuralVariantAnnotation/R/StructuralVariantAnnotation.rdx │ │ │ +-rw-r--r-- 0 root (0) root (0) 130236 2026-08-12 10:54:19.000000 ./usr/lib/R/site-library/StructuralVariantAnnotation/R/StructuralVariantAnnotation.rdb │ │ │ +-rw-r--r-- 0 root (0) root (0) 1524 2026-08-12 10:54:19.000000 ./usr/lib/R/site-library/StructuralVariantAnnotation/R/StructuralVariantAnnotation.rdx │ │ │ -rw-r--r-- 0 root (0) root (0) 587 2026-08-12 10:54:19.000000 ./usr/lib/R/site-library/StructuralVariantAnnotation/README.md │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 10:54:19.000000 ./usr/lib/R/site-library/StructuralVariantAnnotation/doc/ │ │ │ --rw-r--r-- 0 root (0) root (0) 1645 2026-08-12 10:54:19.000000 ./usr/lib/R/site-library/StructuralVariantAnnotation/doc/index.html │ │ │ +-rw-r--r-- 0 root (0) root (0) 1226 2026-08-12 10:54:19.000000 ./usr/lib/R/site-library/StructuralVariantAnnotation/doc/index.html │ │ │ -rw-r--r-- 0 root (0) root (0) 6592 2026-08-12 10:54:19.000000 ./usr/lib/R/site-library/StructuralVariantAnnotation/doc/vignettes.R │ │ │ -rw-r--r-- 0 root (0) root (0) 18528 2026-08-12 10:54:19.000000 ./usr/lib/R/site-library/StructuralVariantAnnotation/doc/vignettes.Rmd │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 10:54:19.000000 ./usr/lib/R/site-library/StructuralVariantAnnotation/extdata/ │ │ │ -rw-r--r-- 0 root (0) root (0) 7215 2026-08-12 10:54:19.000000 ./usr/lib/R/site-library/StructuralVariantAnnotation/extdata/COLO829.10X.longranger.largeSVs.vcf │ │ │ -rw-r--r-- 0 root (0) root (0) 5085 2026-08-12 10:54:19.000000 ./usr/lib/R/site-library/StructuralVariantAnnotation/extdata/COLO829.nanopore.sniffles.vcf │ │ │ -rw-r--r-- 0 root (0) root (0) 34833 2026-08-12 10:54:19.000000 ./usr/lib/R/site-library/StructuralVariantAnnotation/extdata/COLO829T.purple.sv.ann.vcf.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 6239 2026-08-12 10:54:19.000000 ./usr/lib/R/site-library/StructuralVariantAnnotation/extdata/MT.vcf │ │ │ @@ -53,18 +52,18 @@ │ │ │ -rw-r--r-- 0 root (0) root (0) 1738 2026-08-12 10:54:19.000000 ./usr/lib/R/site-library/StructuralVariantAnnotation/extdata/simple.vcf │ │ │ -rw-r--r-- 0 root (0) root (0) 2128 2026-08-12 10:54:19.000000 ./usr/lib/R/site-library/StructuralVariantAnnotation/extdata/tigra-0.3.7.vcf │ │ │ -rw-r--r-- 0 root (0) root (0) 24631 2026-08-12 10:54:19.000000 ./usr/lib/R/site-library/StructuralVariantAnnotation/extdata/truthset_somaticSVs_COLO829.vcf │ │ │ -rw-r--r-- 0 root (0) root (0) 101 2026-08-12 10:54:19.000000 ./usr/lib/R/site-library/StructuralVariantAnnotation/extdata/unnamed.bedpe │ │ │ -rw-r--r-- 0 root (0) root (0) 2591 2026-08-12 10:54:19.000000 ./usr/lib/R/site-library/StructuralVariantAnnotation/extdata/vcf4.2.example.sv.vcf │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 10:54:19.000000 ./usr/lib/R/site-library/StructuralVariantAnnotation/help/ │ │ │ -rw-r--r-- 0 root (0) root (0) 1200 2026-08-12 10:54:19.000000 ./usr/lib/R/site-library/StructuralVariantAnnotation/help/AnIndex │ │ │ --rw-r--r-- 0 root (0) root (0) 44350 2026-08-12 10:54:19.000000 ./usr/lib/R/site-library/StructuralVariantAnnotation/help/StructuralVariantAnnotation.rdb │ │ │ --rw-r--r-- 0 root (0) root (0) 742 2026-08-12 10:54:19.000000 ./usr/lib/R/site-library/StructuralVariantAnnotation/help/StructuralVariantAnnotation.rdx │ │ │ +-rw-r--r-- 0 root (0) root (0) 44994 2026-08-12 10:54:19.000000 ./usr/lib/R/site-library/StructuralVariantAnnotation/help/StructuralVariantAnnotation.rdb │ │ │ +-rw-r--r-- 0 root (0) root (0) 741 2026-08-12 10:54:19.000000 ./usr/lib/R/site-library/StructuralVariantAnnotation/help/StructuralVariantAnnotation.rdx │ │ │ -rw-r--r-- 0 root (0) root (0) 434 2026-08-12 10:54:19.000000 ./usr/lib/R/site-library/StructuralVariantAnnotation/help/aliases.rds │ │ │ --rw-r--r-- 0 root (0) root (0) 410 2026-08-12 10:54:19.000000 ./usr/lib/R/site-library/StructuralVariantAnnotation/help/paths.rds │ │ │ +-rw-r--r-- 0 root (0) root (0) 430 2026-08-12 10:54:19.000000 ./usr/lib/R/site-library/StructuralVariantAnnotation/help/paths.rds │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 10:54:19.000000 ./usr/lib/R/site-library/StructuralVariantAnnotation/html/ │ │ │ -rw-r--r-- 0 root (0) root (0) 6289 2026-08-12 10:54:19.000000 ./usr/lib/R/site-library/StructuralVariantAnnotation/html/00Index.html │ │ │ -rw-r--r-- 0 root (0) root (0) 2133 2026-08-12 10:54:19.000000 ./usr/lib/R/site-library/StructuralVariantAnnotation/html/R.css │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 10:54:19.000000 ./usr/share/ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 10:54:19.000000 ./usr/share/doc/ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 10:54:19.000000 ./usr/share/doc/r-bioc-structuralvariantannotation/ │ │ │ -rw-r--r-- 0 root (0) root (0) 902 2026-08-12 10:54:19.000000 ./usr/share/doc/r-bioc-structuralvariantannotation/changelog.Debian.gz │ │ ├── ./usr/lib/R/site-library/StructuralVariantAnnotation/R/StructuralVariantAnnotation.rdb │ │ │ ├── Rscript --vanilla - {} │ │ │ │ @@ -977,15 +977,15 @@ │ │ │ │ "imports" = " Biostrings = c(subseq = "subseq"), dplyr = c("%>%" = "%>%"), " │ │ │ │ "imports" = " methods = c(as = "as"), methods = c(is = "is"), methods = c(setGeneric = "setGeneric"), " │ │ │ │ "imports" = " methods = c(setMethod = "setMethod"), pwalign = c(deletion = "deletion"), " │ │ │ │ "imports" = " pwalign = c(insertion = "insertion"), pwalign = c(nindel = "nindel"), " │ │ │ │ "imports" = " pwalign = c(nucleotideSubstitutionMatrix = "nucleotideSubstitutionMatrix"), " │ │ │ │ "imports" = " pwalign = c(pairwiseAlignment = "pairwiseAlignment"), rlang = c(.data = ".data"))" │ │ │ │ "lazydata" = "" │ │ │ │ - "path" = ""/home/moeller/Salsa/r-bioc-structuralvariantannotation/debian/r-bioc-structuralvariantannotation/usr/lib/R/site-library/StructuralVariantAnnotation"" │ │ │ │ + "path" = ""/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/debian/r-bioc-structuralvariantannotation/usr/lib/R/site-library/StructuralVariantAnnotation"" │ │ │ │ "spec" = "c(name = "StructuralVariantAnnotation", version = "1.28.0")" │ │ │ │ } │ │ │ │ │ │ │ │ .__S3MethodsTable__. (environment) = │ │ │ │ { │ │ │ │ } │ │ ├── ./usr/lib/R/site-library/StructuralVariantAnnotation/R/StructuralVariantAnnotation.rdx │ │ │ ├── StructuralVariantAnnotation.rdx-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,292 +1,292 @@ │ │ │ │ │ $variables │ │ │ │ │ $variables$.__NAMESPACE__. │ │ │ │ │ -[1] 13676 52 │ │ │ │ │ +[1] 13687 52 │ │ │ │ │ │ │ │ │ │ $variables$.__S3MethodsTable__. │ │ │ │ │ -[1] 13859 52 │ │ │ │ │ +[1] 13870 52 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__.unXStringSet:StructuralVariantAnnotation` │ │ │ │ │ -[1] 15783 52 │ │ │ │ │ +[1] 15794 52 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__breakendRanges:StructuralVariantAnnotation` │ │ │ │ │ -[1] 17550 52 │ │ │ │ │ +[1] 17561 52 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__breakpointRanges:StructuralVariantAnnotation` │ │ │ │ │ -[1] 19223 53 │ │ │ │ │ +[1] 19234 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__elementExtract:StructuralVariantAnnotation` │ │ │ │ │ -[1] 25067 53 │ │ │ │ │ +[1] 25078 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__isStructural:StructuralVariantAnnotation` │ │ │ │ │ -[1] 27497 53 │ │ │ │ │ +[1] 27508 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__isSymbolic:StructuralVariantAnnotation` │ │ │ │ │ -[1] 29871 53 │ │ │ │ │ +[1] 29882 53 │ │ │ │ │ │ │ │ │ │ $variables$.assertValidBreakpointGRanges │ │ │ │ │ -[1] 29924 1455 │ │ │ │ │ +[1] 29935 1455 │ │ │ │ │ │ │ │ │ │ $variables$.breakpointRanges │ │ │ │ │ -[1] 31379 23242 │ │ │ │ │ +[1] 31390 23242 │ │ │ │ │ │ │ │ │ │ $variables$.calc_right_confidence_interval │ │ │ │ │ -[1] 54621 1231 │ │ │ │ │ +[1] 54632 1231 │ │ │ │ │ │ │ │ │ │ $variables$.combineMatchingTranscripts │ │ │ │ │ -[1] 55852 785 │ │ │ │ │ +[1] 55863 785 │ │ │ │ │ │ │ │ │ │ $variables$.constrict │ │ │ │ │ -[1] 56637 1630 │ │ │ │ │ +[1] 56648 1630 │ │ │ │ │ │ │ │ │ │ $variables$.dispatchPerAllele_CollapsedVCF │ │ │ │ │ -[1] 58267 803 │ │ │ │ │ +[1] 58278 803 │ │ │ │ │ │ │ │ │ │ $variables$.dispatchPerAllele_ExpandedVCF │ │ │ │ │ -[1] 59070 540 │ │ │ │ │ +[1] 59081 540 │ │ │ │ │ │ │ │ │ │ $variables$.distance │ │ │ │ │ -[1] 59610 644 │ │ │ │ │ +[1] 59621 644 │ │ │ │ │ │ │ │ │ │ $variables$.elementExtract.ANY │ │ │ │ │ -[1] 60254 730 │ │ │ │ │ +[1] 60265 730 │ │ │ │ │ │ │ │ │ │ $variables$.elementExtract.List │ │ │ │ │ -[1] 60984 959 │ │ │ │ │ +[1] 60995 959 │ │ │ │ │ │ │ │ │ │ $variables$.elementExtract.XStringSet │ │ │ │ │ -[1] 61943 339 │ │ │ │ │ +[1] 61954 339 │ │ │ │ │ │ │ │ │ │ $variables$.expectMetadataInfo │ │ │ │ │ -[1] 62282 662 │ │ │ │ │ +[1] 62293 662 │ │ │ │ │ │ │ │ │ │ $variables$.findOverlaps_queryIns_subjectDup │ │ │ │ │ -[1] 62944 1559 │ │ │ │ │ +[1] 62955 1559 │ │ │ │ │ │ │ │ │ │ $variables$.hasMetadataInfo │ │ │ │ │ -[1] 64503 353 │ │ │ │ │ +[1] 64514 353 │ │ │ │ │ │ │ │ │ │ $variables$.hasSingleAllelePerRecord │ │ │ │ │ -[1] 64856 511 │ │ │ │ │ +[1] 64867 511 │ │ │ │ │ │ │ │ │ │ $variables$.isStructural │ │ │ │ │ -[1] 65367 773 │ │ │ │ │ +[1] 65378 773 │ │ │ │ │ │ │ │ │ │ $variables$.isSymbolic │ │ │ │ │ -[1] 66140 471 │ │ │ │ │ +[1] 66151 471 │ │ │ │ │ │ │ │ │ │ $variables$.mtLen │ │ │ │ │ -[1] 66611 1648 │ │ │ │ │ +[1] 66622 1648 │ │ │ │ │ │ │ │ │ │ $variables$.packageName │ │ │ │ │ -[1] 68259 72 │ │ │ │ │ +[1] 68270 72 │ │ │ │ │ │ │ │ │ │ $variables$.pairwiseLCPrefix │ │ │ │ │ -[1] 68331 995 │ │ │ │ │ +[1] 68342 995 │ │ │ │ │ │ │ │ │ │ $variables$.replaceNa │ │ │ │ │ -[1] 69326 585 │ │ │ │ │ +[1] 69337 585 │ │ │ │ │ │ │ │ │ │ $variables$.replaceNull │ │ │ │ │ -[1] 69911 275 │ │ │ │ │ +[1] 69922 275 │ │ │ │ │ │ │ │ │ │ $variables$.scoreByTranscripts │ │ │ │ │ -[1] 70186 1092 │ │ │ │ │ +[1] 70197 1092 │ │ │ │ │ │ │ │ │ │ $variables$.svLen │ │ │ │ │ -[1] 71278 1135 │ │ │ │ │ +[1] 71289 1135 │ │ │ │ │ │ │ │ │ │ $variables$.testfile │ │ │ │ │ -[1] 72413 728 │ │ │ │ │ +[1] 72424 728 │ │ │ │ │ │ │ │ │ │ $variables$.testrecord │ │ │ │ │ -[1] 73141 1506 │ │ │ │ │ +[1] 73152 1506 │ │ │ │ │ │ │ │ │ │ $variables$.testrecordv44 │ │ │ │ │ -[1] 74647 2187 │ │ │ │ │ +[1] 74658 2187 │ │ │ │ │ │ │ │ │ │ $variables$.toVcfBreakendNotationAlt │ │ │ │ │ -[1] 76834 1875 │ │ │ │ │ +[1] 76845 1875 │ │ │ │ │ │ │ │ │ │ $variables$.traversable_segments │ │ │ │ │ -[1] 78709 1986 │ │ │ │ │ +[1] 78720 1986 │ │ │ │ │ │ │ │ │ │ $variables$.unXStringSet │ │ │ │ │ -[1] 80695 435 │ │ │ │ │ +[1] 80706 435 │ │ │ │ │ │ │ │ │ │ $variables$.vcfAltToStrandPair │ │ │ │ │ -[1] 81130 587 │ │ │ │ │ +[1] 81141 587 │ │ │ │ │ │ │ │ │ │ $variables$align_breakpoints │ │ │ │ │ -[1] 81717 4182 │ │ │ │ │ +[1] 81728 4182 │ │ │ │ │ │ │ │ │ │ $variables$breakendRanges │ │ │ │ │ -[1] 85899 440 │ │ │ │ │ +[1] 85910 440 │ │ │ │ │ │ │ │ │ │ $variables$breakpointGRangesToVCF │ │ │ │ │ -[1] 86339 2222 │ │ │ │ │ +[1] 86350 2222 │ │ │ │ │ │ │ │ │ │ $variables$breakpointRanges │ │ │ │ │ -[1] 88561 444 │ │ │ │ │ +[1] 88572 444 │ │ │ │ │ │ │ │ │ │ $variables$breakpointgr2bedpe │ │ │ │ │ -[1] 89005 1270 │ │ │ │ │ +[1] 89016 1270 │ │ │ │ │ │ │ │ │ │ $variables$breakpointgr2pairs │ │ │ │ │ -[1] 90275 1723 │ │ │ │ │ +[1] 90286 1723 │ │ │ │ │ │ │ │ │ │ $variables$calculateReferenceHomology │ │ │ │ │ -[1] 91998 3141 │ │ │ │ │ +[1] 92009 3141 │ │ │ │ │ │ │ │ │ │ $variables$countBreakpointOverlaps │ │ │ │ │ -[1] 95139 1665 │ │ │ │ │ +[1] 95150 1665 │ │ │ │ │ │ │ │ │ │ $variables$elementExtract │ │ │ │ │ -[1] 96804 452 │ │ │ │ │ +[1] 96815 452 │ │ │ │ │ │ │ │ │ │ $variables$extractBreakpointSequence │ │ │ │ │ -[1] 97256 1020 │ │ │ │ │ +[1] 97267 1020 │ │ │ │ │ │ │ │ │ │ $variables$extractReferenceSequence │ │ │ │ │ -[1] 98276 2288 │ │ │ │ │ +[1] 98287 2288 │ │ │ │ │ │ │ │ │ │ $variables$findBreakpointOverlaps │ │ │ │ │ -[1] 100564 2761 │ │ │ │ │ +[1] 100575 2761 │ │ │ │ │ │ │ │ │ │ $variables$findInsDupOverlaps │ │ │ │ │ -[1] 103325 2171 │ │ │ │ │ +[1] 103336 2171 │ │ │ │ │ │ │ │ │ │ $variables$findTransitiveCalls │ │ │ │ │ -[1] 105496 7011 │ │ │ │ │ +[1] 105507 7011 │ │ │ │ │ │ │ │ │ │ $variables$hasPartner │ │ │ │ │ -[1] 112507 511 │ │ │ │ │ +[1] 112518 511 │ │ │ │ │ │ │ │ │ │ $variables$header.Type.Character │ │ │ │ │ -[1] 113018 54 │ │ │ │ │ +[1] 113029 54 │ │ │ │ │ │ │ │ │ │ $variables$header.Type.Flag │ │ │ │ │ -[1] 113072 49 │ │ │ │ │ +[1] 113083 49 │ │ │ │ │ │ │ │ │ │ $variables$header.Type.Float │ │ │ │ │ -[1] 113121 49 │ │ │ │ │ +[1] 113132 49 │ │ │ │ │ │ │ │ │ │ $variables$header.Type.Integer │ │ │ │ │ -[1] 113170 52 │ │ │ │ │ +[1] 113181 52 │ │ │ │ │ │ │ │ │ │ $variables$header.Type.String │ │ │ │ │ -[1] 113222 51 │ │ │ │ │ +[1] 113233 51 │ │ │ │ │ │ │ │ │ │ $variables$isStructural │ │ │ │ │ -[1] 113273 428 │ │ │ │ │ +[1] 113284 428 │ │ │ │ │ │ │ │ │ │ $variables$isSymbolic │ │ │ │ │ -[1] 113701 434 │ │ │ │ │ +[1] 113712 434 │ │ │ │ │ │ │ │ │ │ $variables$numtDetect │ │ │ │ │ -[1] 114135 3309 │ │ │ │ │ +[1] 114146 3309 │ │ │ │ │ │ │ │ │ │ $variables$pairs2breakpointgr │ │ │ │ │ -[1] 117444 2282 │ │ │ │ │ +[1] 117455 2282 │ │ │ │ │ │ │ │ │ │ $variables$partner │ │ │ │ │ -[1] 119726 572 │ │ │ │ │ +[1] 119737 572 │ │ │ │ │ │ │ │ │ │ $variables$rtDetect │ │ │ │ │ -[1] 120298 7580 │ │ │ │ │ +[1] 120309 7580 │ │ │ │ │ │ │ │ │ │ $variables$simpleEventLength │ │ │ │ │ -[1] 127878 1139 │ │ │ │ │ +[1] 127889 1139 │ │ │ │ │ │ │ │ │ │ $variables$simpleEventType │ │ │ │ │ -[1] 129017 1208 │ │ │ │ │ +[1] 129028 1208 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $references │ │ │ │ │ $references$`env::1` │ │ │ │ │ -[1] 305 13371 │ │ │ │ │ +[1] 305 13382 │ │ │ │ │ │ │ │ │ │ $references$`env::10` │ │ │ │ │ -[1] 16793 278 │ │ │ │ │ +[1] 16804 278 │ │ │ │ │ │ │ │ │ │ $references$`env::11` │ │ │ │ │ -[1] 15835 479 │ │ │ │ │ +[1] 15846 479 │ │ │ │ │ │ │ │ │ │ $references$`env::12` │ │ │ │ │ -[1] 16314 479 │ │ │ │ │ +[1] 16325 479 │ │ │ │ │ │ │ │ │ │ $references$`env::13` │ │ │ │ │ -[1] 18776 447 │ │ │ │ │ +[1] 18787 447 │ │ │ │ │ │ │ │ │ │ $references$`env::14` │ │ │ │ │ -[1] 18496 280 │ │ │ │ │ +[1] 18507 280 │ │ │ │ │ │ │ │ │ │ $references$`env::15` │ │ │ │ │ -[1] 17602 447 │ │ │ │ │ +[1] 17613 447 │ │ │ │ │ │ │ │ │ │ $references$`env::16` │ │ │ 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│
│ │ │
│ │ │ [Up] │ │ │ [Top] │ │ │
│ │ │

Vignettes from package 'StructuralVariantAnnotation'

│ │ │ - │ │ │ -│ │ │ -│ │ │ -│ │ │ -│ │ │ -│ │ │ -│ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
StructuralVariantAnnotation::Structural Variant Annotation Packagesource
│ │ │ +The package contains no vignette meta-information. │ │ │

Other files in the doc directory

│ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ + │ │ │
vignettes.R
vignettes.Rmd
│ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,7 +1,8 @@ │ │ │ │ ************ VViiggnneetttteess aanndd ootthheerr ddooccuummeennttaattiioonn[[[[RR llooggoo]]]] ************ │ │ │ │ =============================================================================== │ │ │ │ _[_[_U_p_]_]_[_[_T_o_p_]_] │ │ │ │ ********** VViiggnneetttteess ffrroomm ppaacckkaaggee ''SSttrruuccttuurraallVVaarriiaannttAAnnnnoottaattiioonn'' ********** │ │ │ │ -_S_t_r_u_c_t_u_r_a_l_V_a_r_i_a_n_t_A_n_n_o_t_a_t_i_o_n_:_: Structural Variant Annotation Package _s_o_u_r_c_e │ │ │ │ +The package contains no vignette meta-information. │ │ │ │ ********** OOtthheerr ffiilleess iinn tthhee ddoocc ddiirreeccttoorryy ********** │ │ │ │ _v_i_g_n_e_t_t_e_s_._R │ │ │ │ + _v_i_g_n_e_t_t_e_s_._R_m_d │ │ ├── ./usr/lib/R/site-library/StructuralVariantAnnotation/help/StructuralVariantAnnotation.rdb │ │ │ ├── Rscript --vanilla - {} │ │ │ │ @@ -8,15 +8,15 @@ │ │ │ │ structure("takes a `GRanges` based breakend-centric approach.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("* Parse VCF objects with the `breakpointRanges()` and `breakendRanges()`functions.\n", Rd_tag = "TEXT"), │ │ │ │ structure(" * Find breakpoint overlaps with the `findBreakpointOverlaps()`\n", Rd_tag = "TEXT"), │ │ │ │ structure(" and `countBreakpointOverlaps()` functions.\n", Rd_tag = "TEXT"), │ │ │ │ structure(" * Generate BEDPE files for circos plot with `breakpointgr2pairs()` function.\n", Rd_tag = "TEXT"), │ │ │ │ structure(" * ...\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure("For more details on the features of StructuralVariantAnnotation, read the vignette:\n", Rd_tag = "TEXT"), │ │ │ │ - structure("`browseVignettes(package = \"StructuralVariantAnnotation\")`\n", Rd_tag = "TEXT")), Rd_tag = "\\details")), Rdfile = "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/StructuralVariantAnnotation.Rd", class = "Rd", meta = list( │ │ │ │ + structure("`browseVignettes(package = \"StructuralVariantAnnotation\")`\n", Rd_tag = "TEXT")), Rd_tag = "\\details")), Rdfile = "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/StructuralVariantAnnotation.Rd", class = "Rd", meta = list( │ │ │ │ docType = "package", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ align_breakpoints (list) = structure(list(structure(list(structure("Adjusting the nominal position of a pair of partnered breakpoint.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("align_breakpoints", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("align_breakpoints", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Adjusting the nominal position of a pair of partnered breakpoint.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("align_breakpoints(\n", Rd_tag = "RCODE"), │ │ │ │ @@ -28,15 +28,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("align", Rd_tag = "TEXT")), │ │ │ │ list(structure("The alignment type.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("is_higher_breakend", Rd_tag = "TEXT")), │ │ │ │ list(structure("Breakpoint ID ordering.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "TEXT"), structure("A VCF object with adjusted nominal positions.\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/align_breakpoints.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "TEXT"), structure("A VCF object with adjusted nominal positions.\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/align_breakpoints.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ breakendRanges (list) = structure(list(structure(list(structure("Extracting unpartnered breakend structural variants as a GRanges", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("breakendRanges", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("breakendRanges", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("breakendRanges,VCF-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Extracting unpartnered breakend structural variants as a GRanges\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -70,15 +70,15 @@ │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure("VCF", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(": Extracting unpartnered structural variants as \n", Rd_tag = "TEXT"), │ │ │ │ structure("GRanges.\n", Rd_tag = "TEXT")), Rd_tag = "\\itemize"))), Rd_tag = "\\section"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("vcf.file <- system.file(\"extdata\", \"gridss.vcf\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" package = \"StructuralVariantAnnotation\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("vcf <- VariantAnnotation::readVcf(vcf.file, \"hg19\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("breakendRanges(vcf)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("breakendRanges(vcf, nominalPosition=TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/breakendRanges.Rd", class = "Rd", meta = list( │ │ │ │ + structure("breakendRanges(vcf, nominalPosition=TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/breakendRanges.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ breakpointGRangesToVCF (list) = structure(list(structure(list(structure("Converts the given breakpoint GRanges object to VCF format in breakend\n", Rd_tag = "TEXT"), │ │ │ │ structure("notation.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("breakpointGRangesToVCF", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("breakpointGRangesToVCF", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Converts the given breakpoint GRanges object to VCF format in breakend\n", Rd_tag = "TEXT"), │ │ │ │ @@ -89,15 +89,15 @@ │ │ │ │ structure("breakend SV records.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("...", Rd_tag = "TEXT")), │ │ │ │ list(structure("For cbind and rbind a list of VCF objects. For all other methods \n", Rd_tag = "TEXT"), │ │ │ │ structure("... are additional arguments passed to methods. See VCF class in \n", Rd_tag = "TEXT"), │ │ │ │ structure("VariantAnnotation for more details.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "TEXT"), structure("A VCF object.\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/breakpointGRangesToVCF.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "TEXT"), structure("A VCF object.\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/breakpointGRangesToVCF.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ breakpointRanges (list) = structure(list(structure(list(structure("Extracting the structural variants as a GRanges.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("breakpointRanges", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("breakpointRanges", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("breakpointRanges,VCF-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure(".breakpointRanges", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -177,15 +177,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(list(), Rd_tag = "\\item"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure("VCF", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(": Extracting structural variants as GRanges.\n", Rd_tag = "TEXT")), Rd_tag = "\\itemize"))), Rd_tag = "\\section"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("vcf.file <- system.file(\"extdata\", \"vcf4.2.example.sv.vcf\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" package = \"StructuralVariantAnnotation\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("vcf <- VariantAnnotation::readVcf(vcf.file, \"hg19\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("breakpointRanges(vcf)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("breakpointRanges(vcf, nominalPosition=TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/breakpointRanges.Rd", class = "Rd", meta = list( │ │ │ │ + structure("breakpointRanges(vcf, nominalPosition=TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/breakpointRanges.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ breakpointgr2bedpe (list) = structure(list(structure(list(structure("Converting breakpoint GRanges to BEDPE-like dataframe", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("breakpointgr2bedpe", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("breakpointgr2bedpe", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Converting breakpoint GRanges to BEDPE-like dataframe\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("breakpointgr2bedpe(gr)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -200,15 +200,15 @@ │ │ │ │ structure("See ", Rd_tag = "TEXT"), structure(list(structure("https://bedtools.readthedocs.io/en/latest/content/general-usage.html", Rd_tag = "VERB")), Rd_tag = "\\url"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("for more details on the BEDPE format.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("A BEDPE-formatted data frame.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("#coverting a GRanges object to BEDPE-like dataframe\n", Rd_tag = "RCODE"), │ │ │ │ structure("vcf.file <- system.file(\"extdata\", \"gridss.vcf\", package = \"StructuralVariantAnnotation\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("vcf <- VariantAnnotation::readVcf(vcf.file, \"hg19\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("gr <- breakpointRanges(vcf)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("breakpointgr2bedpe(gr)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/breakpointgr2bedpe.Rd", class = "Rd", meta = list( │ │ │ │ + structure("breakpointgr2bedpe(gr)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/breakpointgr2bedpe.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ calculateReferenceHomology (list) = structure(list(structure(list(structure("Calculates the length of inexact homology between the breakpoint sequence\n", Rd_tag = "TEXT"), │ │ │ │ structure("and the reference", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("calculateReferenceHomology", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("calculateReferenceHomology", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculates the length of inexact homology between the breakpoint sequence\n", Rd_tag = "TEXT"), │ │ │ │ @@ -242,15 +242,15 @@ │ │ │ │ structure(list(list(structure("gapOpening", Rd_tag = "TEXT")), │ │ │ │ list(structure("see pwalign::pairwiseAlignment", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("gapExtension", Rd_tag = "TEXT")), │ │ │ │ list(structure("see pwalign::pairwiseAlignment", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("A dataframe containing the length of inexact homology between the \n", Rd_tag = "TEXT"), │ │ │ │ - structure("breakpoint sequence and the reference.\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/calculateReferenceHomology.Rd", class = "Rd", meta = list( │ │ │ │ + structure("breakpoint sequence and the reference.\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/calculateReferenceHomology.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ countBreakpointOverlaps (list) = structure(list(structure(list(structure("Counting overlapping breakpoints between two breakpoint sets", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("countBreakpointOverlaps", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("countBreakpointOverlaps", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Counting overlapping breakpoints between two breakpoint sets\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("countBreakpointOverlaps(\n", Rd_tag = "RCODE"), │ │ │ │ @@ -286,30 +286,30 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("An integer vector containing the tabulated query overlap hits.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("truth_vcf = VariantAnnotation::readVcf(system.file(\"extdata\", \"na12878_chr22_Sudmunt2015.vcf\", \n", Rd_tag = "RCODE"), │ │ │ │ structure("package = \"StructuralVariantAnnotation\"))\n", Rd_tag = "RCODE"), │ │ │ │ structure("crest_vcf = VariantAnnotation::readVcf(system.file(\"extdata\", \"na12878_chr22_crest.vcf\", \n", Rd_tag = "RCODE"), │ │ │ │ structure("package = \"StructuralVariantAnnotation\"))\n", Rd_tag = "RCODE"), │ │ │ │ structure("caller_bpgr = breakpointRanges(crest_vcf)\n", Rd_tag = "RCODE"), │ │ │ │ structure("caller_bpgr$true_positive = countBreakpointOverlaps(caller_bpgr, breakpointRanges(truth_vcf),\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" maxgap=100, sizemargin=0.25, restrictMarginToSizeMultiple=0.5, countOnlyBest=TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/countBreakpointOverlaps.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" maxgap=100, sizemargin=0.25, restrictMarginToSizeMultiple=0.5, countOnlyBest=TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/countBreakpointOverlaps.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ elementExtract (list) = structure(list(structure(list(structure("Extracts the element of each element at the given position", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("elementExtract", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("elementExtract", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("internal", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Extracts the element of each element at the given position\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("elementExtract(x, offset = 1)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ list(structure("x", Rd_tag = "TEXT")), list(structure("list-like object", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("offset", Rd_tag = "TEXT")), │ │ │ │ list(structure("offset of list", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "TEXT"), structure("The element of each element at given positions.\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/elementExtract.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "TEXT"), structure("The element of each element at given positions.\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/elementExtract.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractBreakpointSequence (list) = structure(list(structure(list(structure("Extracts the breakpoint sequence.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractBreakpointSequence", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractBreakpointSequence", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Extracts the breakpoint sequence.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractBreakpointSequence(gr, ref, anchoredBases, remoteBases = anchoredBases)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -324,15 +324,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("remoteBases", Rd_tag = "TEXT")), │ │ │ │ list(structure("Number of bases from other side of breakpoint to extract", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("The sequence is the sequenced traversed from the reference anchor bases\n", Rd_tag = "TEXT"), │ │ │ │ structure("to the breakpoint. For backward (-) breakpoints, this corresponds to the\n", Rd_tag = "TEXT"), │ │ │ │ structure("reverse compliment of the reference sequence bases.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "TEXT"), structure("Breakpoint sequence around the variant position.\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/extractBreakpointSequence.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "TEXT"), structure("Breakpoint sequence around the variant position.\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/extractBreakpointSequence.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractReferenceSequence (list) = structure(list(structure(list(structure("Returns the reference sequence around the breakpoint position", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractReferenceSequence", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractReferenceSequence", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Returns the reference sequence around the breakpoint position\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractReferenceSequence(\n", Rd_tag = "RCODE"), │ │ │ │ @@ -350,15 +350,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("followingBases", Rd_tag = "TEXT")), │ │ │ │ list(structure("Number of reference bases past breakpoint to extract", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("The sequence is the sequenced traversed from the reference anchor bases\n", Rd_tag = "TEXT"), │ │ │ │ structure("to the breakpoint. For backward (-) breakpoints, this corresponds to the\n", Rd_tag = "TEXT"), │ │ │ │ structure("reverse compliment of the reference sequence bases.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "TEXT"), structure("Reference sequence around the breakpoint position.\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/extractReferenceSequence.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "TEXT"), structure("Reference sequence around the breakpoint position.\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/extractReferenceSequence.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ findBreakpointOverlaps (list) = structure(list(structure(list(structure("Finding overlapping breakpoints between two breakpoint sets", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("findBreakpointOverlaps", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("findBreakpointOverlaps", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Finding overlapping breakpoints between two breakpoint sets\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("findBreakpointOverlaps(\n", Rd_tag = "RCODE"), │ │ │ │ @@ -421,15 +421,15 @@ │ │ │ │ structure("subject.vcf <- VariantAnnotation::readVcf(subject.file, \"hg19\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("#parsing vcfs to GRanges objects\n", Rd_tag = "RCODE"), │ │ │ │ structure("query.gr <- breakpointRanges(query.vcf)\n", Rd_tag = "RCODE"), │ │ │ │ structure("subject.gr <- breakpointRanges(subject.vcf)\n", Rd_tag = "RCODE"), │ │ │ │ structure("#find overlapping breakpoint intervals\n", Rd_tag = "RCODE"), │ │ │ │ structure("findBreakpointOverlaps(query.gr, subject.gr)\n", Rd_tag = "RCODE"), │ │ │ │ structure("findBreakpointOverlaps(query.gr, subject.gr, ignore.strand=TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("findBreakpointOverlaps(query.gr, subject.gr, maxgap=100, sizemargin=0.5)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/findBreakpointOverlaps.Rd", class = "Rd", meta = list( │ │ │ │ + structure("findBreakpointOverlaps(query.gr, subject.gr, maxgap=100, sizemargin=0.5)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/findBreakpointOverlaps.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ findInsDupOverlaps (list) = structure(list(structure(list(structure("Finds duplication events that are reported as inserts.\n", Rd_tag = "TEXT"), │ │ │ │ structure("As sequence alignment algorithms do no allow backtracking, long read-based\n", Rd_tag = "TEXT"), │ │ │ │ structure("variant callers will frequently report small duplication as insertion events.\n", Rd_tag = "TEXT"), │ │ │ │ structure("Whilst both the duplication and insertion representations result in the same\n", Rd_tag = "TEXT"), │ │ │ │ structure("sequence, this representational difference is problematic when comparing\n", Rd_tag = "TEXT"), │ │ │ │ @@ -447,15 +447,15 @@ │ │ │ │ structure(list(list(structure("maxgap", Rd_tag = "TEXT")), │ │ │ │ list(structure("maximum distance between the insertion position and the duplication", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("maxsizedifference", Rd_tag = "TEXT")), │ │ │ │ list(structure("maximum size difference between the duplication and insertion.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Hits object containing the ordinals of the matching breakends\n", Rd_tag = "TEXT"), │ │ │ │ - structure("in the query and subject\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/findInsDupOverlaps.Rd", class = "Rd", meta = list( │ │ │ │ + structure("in the query and subject\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/findInsDupOverlaps.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ findTransitiveCalls (list) = structure(list(structure(list(structure("Identifies potential transitive imprecise calls that can be explained by\n", Rd_tag = "TEXT"), │ │ │ │ structure("traversing multiple breakpoints.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("findTransitiveCalls", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("findTransitiveCalls", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Transitive calls are imprecise breakpoints or breakpoints with inserted sequence\n", Rd_tag = "TEXT"), │ │ │ │ @@ -526,15 +526,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("`DataFrame` containing the transitive calls traversed with the following columns:\n", Rd_tag = "TEXT"), │ │ │ │ structure("| column | meaning | \n", Rd_tag = "TEXT"), │ │ │ │ structure("| ------ | ------- | \n", Rd_tag = "TEXT"), │ │ │ │ structure("| transitive_breakpoint_name | Name of the transitive breakpoint a path was found for |\n", Rd_tag = "TEXT"), │ │ │ │ structure("| total_distance | Total length (in bp) of the path |\n", Rd_tag = "TEXT"), │ │ │ │ structure("| traversed_breakpoint_names | `CharacterList` of names of breakpoint traversed in the path |\n", Rd_tag = "TEXT"), │ │ │ │ - structure("| distance_to_traversed_breakpoint | `IntegerList` of distances from start of path to end of traversing breakpoint |\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/findTransitiveCalls.Rd", class = "Rd", meta = list( │ │ │ │ + structure("| distance_to_traversed_breakpoint | `IntegerList` of distances from start of path to end of traversing breakpoint |\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/findTransitiveCalls.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ hasPartner (list) = structure(list(structure(list(structure("Determines whether this breakend has a valid partner in this\n", Rd_tag = "TEXT"), │ │ │ │ structure("GRanges", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("hasPartner", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("hasPartner", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Determines whether this breakend has a valid partner in this\n", Rd_tag = "TEXT"), │ │ │ │ @@ -552,15 +552,15 @@ │ │ │ │ structure(" package = \"StructuralVariantAnnotation\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("vcf <- VariantAnnotation::readVcf(vcf.file)\n", Rd_tag = "RCODE"), │ │ │ │ structure("gr <- breakpointRanges(vcf)\n", Rd_tag = "RCODE"), │ │ │ │ structure("gr <- gr[seqnames(gr) == \"6\"]\n", Rd_tag = "RCODE"), │ │ │ │ structure("# We now need to filter out inter-chromosomal events to ensure\n", Rd_tag = "RCODE"), │ │ │ │ structure("# our GRanges doesn't contain any breakpoints whose partner\n", Rd_tag = "RCODE"), │ │ │ │ structure("# has already been filtered out and no longer exists in the GRanges.\n", Rd_tag = "RCODE"), │ │ │ │ - structure("gr <- gr[hasPartner(gr)]\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/hasPartner.Rd", class = "Rd", meta = list( │ │ │ │ + structure("gr <- gr[hasPartner(gr)]\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/hasPartner.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ hideOutput (NULL) = NULL │ │ │ │ │ │ │ │ isStructural (list) = structure(list(structure(list(structure("Determining whether the variant is a structural variant", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("isStructural", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("isStructural", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -605,15 +605,15 @@ │ │ │ │ structure("structural variant.\n", Rd_tag = "TEXT"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(list(), Rd_tag = "\\item"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure("VCF", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(": Determining whether a VCF object is a structural\n", Rd_tag = "TEXT"), │ │ │ │ structure("variant.\n", Rd_tag = "TEXT")), Rd_tag = "\\itemize"))), Rd_tag = "\\section"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("vcf.file <- system.file(\"extdata\", \"gridss.vcf\", package = \"StructuralVariantAnnotation\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("vcf <- VariantAnnotation::readVcf(vcf.file, \"hg19\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("isStructural(vcf)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/isStructural.Rd", class = "Rd", meta = list( │ │ │ │ + structure("isStructural(vcf)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/isStructural.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ isSymbolic (list) = structure(list(structure(list(structure("Determining whether the variant is a symbolic allele.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("isSymbolic", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("isSymbolic", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("isSymbolic,CollapsedVCF-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("isSymbolic,ExpandedVCF-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -646,15 +646,15 @@ │ │ │ │ structure("allele. Only single ALT values are accepted.\n", Rd_tag = "TEXT"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(list(), Rd_tag = "\\item"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure("ExpandedVCF", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(": Determining whether a ExpandedVCF object is a symbolic \n", Rd_tag = "TEXT"), │ │ │ │ structure("allele\n", Rd_tag = "TEXT")), Rd_tag = "\\itemize"))), Rd_tag = "\\section"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("vcf.file <- system.file(\"extdata\", \"gridss.vcf\", package = \"StructuralVariantAnnotation\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("vcf <- VariantAnnotation::readVcf(vcf.file, \"hg19\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("isSymbolic(vcf)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/isSymbolic.Rd", class = "Rd", meta = list( │ │ │ │ + structure("isSymbolic(vcf)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/isSymbolic.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ numtDetect (list) = structure(list(structure(list(structure("Detecting nuclear mitochondria fusion events.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("numtDetect", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("numtDetect", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Detecting nuclear mitochondria fusion events.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("numtDetect(gr, nonStandardChromosomes = FALSE, max_ins_dist = 1000)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -673,15 +673,15 @@ │ │ │ │ structure("This function searches for NUMT events by identifying breakpoints supporting the fusion of\n", Rd_tag = "TEXT"), │ │ │ │ structure("nuclear chromosome and mitochondrial genome. Only BND notations are supported at the current stage.\n", Rd_tag = "TEXT"), │ │ │ │ structure("Possible linked nuclear insertion sites are reported using SV IDs in the candidatePartnerId metadata column.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("A GRanges object of possible NUMT loci.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("vcf.file <- system.file(\"extdata\", \"MT.vcf\", package = \"StructuralVariantAnnotation\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("vcf <- VariantAnnotation::readVcf(vcf.file, \"hg19\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("gr <- breakpointRanges(vcf, nominalPosition=TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("numt.gr <- numtDetect(gr)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/numtDetect.Rd", class = "Rd", meta = list( │ │ │ │ + structure("numt.gr <- numtDetect(gr)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/numtDetect.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ pairs2breakpointgr (list) = structure(list(structure(list(structure("Converts a breakpoint GRanges object to a Pairs object", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("breakpointgr2pairs", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("breakpointgr2pairs", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("pairs2breakpointgr", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Converts a breakpoint GRanges object to a Pairs object\n", Rd_tag = "TEXT"), │ │ │ │ @@ -747,15 +747,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("Breakpoint GRanges object.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("vcf.file <- system.file(\"extdata\", \"gridss.vcf\", package = \"StructuralVariantAnnotation\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("bpgr <- breakpointRanges(VariantAnnotation::readVcf(vcf.file))\n", Rd_tag = "RCODE"), │ │ │ │ structure("pairgr <- breakpointgr2pairs(bpgr)\n", Rd_tag = "RCODE"), │ │ │ │ structure("#rtracklayer::export(pairgr, con=\"example.bedpe\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("bedpe.file <- system.file(\"extdata\", \"gridss.bedpe\", package = \"StructuralVariantAnnotation\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("bedpe.pairs <- rtracklayer::import(bedpe.file)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("bedpe.bpgr <- pairs2breakpointgr(bedpe.pairs)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/pairs2breakpointgr.Rd", class = "Rd", meta = list( │ │ │ │ + structure("bedpe.bpgr <- pairs2breakpointgr(bedpe.pairs)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/pairs2breakpointgr.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ partner (list) = structure(list(structure(list(structure("GRanges representing the breakend coordinates of\n", Rd_tag = "TEXT"), │ │ │ │ structure("structural variants\n", Rd_tag = "TEXT"), structure("#@export\n", Rd_tag = "TEXT"), │ │ │ │ structure("Partner breakend for each breakend.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("partner", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("partner", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -775,15 +775,15 @@ │ │ │ │ structure("those in the input object.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("#reading in a VCF file as \\code{vcf}\n", Rd_tag = "RCODE"), │ │ │ │ structure("vcf.file <- system.file(\"extdata\", \"gridss.vcf\", package = \"StructuralVariantAnnotation\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("vcf <- VariantAnnotation::readVcf(vcf.file, \"hg19\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("#parsing \\code{vcf} to GRanges object \\code{gr}\n", Rd_tag = "RCODE"), │ │ │ │ structure("gr <- breakpointRanges(vcf)\n", Rd_tag = "RCODE"), │ │ │ │ structure("#output partner breakend of each breakend in \\code{gr}\n", Rd_tag = "RCODE"), │ │ │ │ - structure("partner(gr)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/partner.Rd", class = "Rd", meta = list( │ │ │ │ + structure("partner(gr)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/partner.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ rtDetect (list) = structure(list(structure(list(structure("Detecting retrotranscript insertion in nuclear genomes.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("rtDetect", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("rtDetect", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Detecting retrotranscript insertion in nuclear genomes.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("rtDetect(gr, genes, maxgap = 100, minscore = 0.3)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -799,15 +799,15 @@ │ │ │ │ structure(list(list(structure("minscore", Rd_tag = "TEXT")), │ │ │ │ list(structure("The minimum proportion of intronic deletions of a transcript should be identified.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function searches for retroposed transcripts by identifying breakpoints supporting \n", Rd_tag = "TEXT"), │ │ │ │ structure("intronic deletions and fusions between exons and remote loci.\n", Rd_tag = "TEXT"), │ │ │ │ structure("Only BND notations are supported at the current stage.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("A GRangesList object, named insSite and rt, reporting breakpoints supporting insert sites and \n", Rd_tag = "TEXT"), │ │ │ │ - structure("retroposed transcripts respectively. 'exon' and 'txs' in the metadata columns report exon_id and transcript_name from the 'genes' object.\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/rtDetect.Rd", class = "Rd", meta = list( │ │ │ │ + structure("retroposed transcripts respectively. 'exon' and 'txs' in the metadata columns report exon_id and transcript_name from the 'genes' object.\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/rtDetect.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ safeDeparse (closure) = function (obj) │ │ │ │ { │ │ │ │ tryCatch({ │ │ │ │ deparse(obj) │ │ │ │ }, error = function(e) { │ │ │ │ @@ -819,15 +819,15 @@ │ │ │ │ structure(list(structure("simpleEventLength", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("simpleEventLength", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Length of event if interpreted as an isolated breakpoint.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("simpleEventLength(gr)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ list(structure("gr", Rd_tag = "TEXT")), list(structure("breakpoint GRanges object", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "TEXT"), structure("Length of the simplest explanation of this breakpoint/breakend.\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/simpleEventLength.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "TEXT"), structure("Length of the simplest explanation of this breakpoint/breakend.\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/simpleEventLength.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ simpleEventType (list) = structure(list(structure(list(structure("Type of simplest explanation of event. Possible types are:\n", Rd_tag = "TEXT"), │ │ │ │ structure("| Type | Description |\n", Rd_tag = "TEXT"), structure("| BND | Single breakend |\n", Rd_tag = "TEXT"), │ │ │ │ structure("| CTX | Interchromosomal translocation |\n", Rd_tag = "TEXT"), │ │ │ │ structure("| INV | Inversion. |\n", Rd_tag = "TEXT"), structure("| DUP | Tandem duplication |\n", Rd_tag = "TEXT"), │ │ │ │ structure("| INS | Insertion |\n", Rd_tag = "TEXT"), structure("| DEL | Deletion |", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ @@ -838,10 +838,10 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ list(structure("gr", Rd_tag = "TEXT")), list(structure("breakpoint GRanges object", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("insertionLengthThreshold", Rd_tag = "TEXT")), │ │ │ │ list(structure("portion of inserted bases compared to total event size to be classified as an insertion.\n", Rd_tag = "TEXT"), │ │ │ │ structure("For example, a 5bp deletion with 5 inserted bases will be classified as an INS event.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "TEXT"), structure("Type of simplest explanation of event\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/simpleEventType.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "TEXT"), structure("Type of simplest explanation of event\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/simpleEventType.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ ├── ./usr/lib/R/site-library/StructuralVariantAnnotation/help/StructuralVariantAnnotation.rdx │ │ │ ├── StructuralVariantAnnotation.rdx-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,145 +1,145 @@ │ │ │ │ │ $variables │ │ │ │ │ $variables$StructuralVariantAnnotation │ │ │ │ │ -[1] 294 1067 │ │ │ │ │ +[1] 308 1080 │ │ │ │ │ │ │ │ │ │ $variables$align_breakpoints │ │ │ │ │ -[1] 1659 1020 │ │ │ │ │ +[1] 1700 1034 │ │ │ │ │ │ │ │ │ │ $variables$breakendRanges │ │ │ │ │ -[1] 2975 1913 │ │ │ │ │ +[1] 3044 1927 │ │ │ │ │ │ │ │ │ │ $variables$breakpointGRangesToVCF │ │ │ │ │ -[1] 5191 1021 │ │ │ │ │ +[1] 5288 1034 │ │ │ │ │ │ │ │ │ │ $variables$breakpointRanges │ │ │ │ │ -[1] 6509 3286 │ │ │ │ │ +[1] 6634 3301 │ │ │ │ │ │ │ │ │ │ $variables$breakpointgr2bedpe │ │ │ │ │ -[1] 10094 1274 │ │ │ │ │ +[1] 10247 1290 │ │ │ │ │ │ │ │ │ │ $variables$calculateReferenceHomology │ │ │ │ │ -[1] 11671 1566 │ │ │ │ │ +[1] 11855 1581 │ │ │ │ │ │ │ │ │ │ $variables$countBreakpointOverlaps │ │ │ │ │ -[1] 13539 1927 │ │ │ │ │ +[1] 13751 1941 │ │ │ │ │ │ │ │ │ │ $variables$elementExtract │ │ │ │ │ -[1] 15760 847 │ │ │ │ │ +[1] 16002 860 │ │ │ │ │ │ │ │ │ │ $variables$extractBreakpointSequence │ │ │ │ │ -[1] 16910 1166 │ │ │ │ │ +[1] 17179 1180 │ │ │ │ │ │ │ │ │ │ $variables$extractReferenceSequence │ │ │ │ │ -[1] 18377 1228 │ │ │ │ │ +[1] 18673 1242 │ │ │ │ │ │ │ │ │ │ $variables$findBreakpointOverlaps │ │ │ │ │ -[1] 19907 2823 │ │ │ │ │ +[1] 20230 2837 │ │ │ │ │ │ │ │ │ │ $variables$findInsDupOverlaps │ │ │ │ │ -[1] 23030 1366 │ │ │ │ │ +[1] 23381 1379 │ │ │ │ │ │ │ │ │ │ $variables$findTransitiveCalls │ │ │ │ │ -[1] 24695 2935 │ │ │ │ │ +[1] 25073 2951 │ │ │ │ │ │ │ │ │ │ $variables$hasPartner │ │ │ │ │ -[1] 27922 1357 │ │ │ │ │ +[1] 28330 1370 │ │ │ │ │ │ │ │ │ │ $variables$isStructural │ │ │ │ │ -[1] 29568 1940 │ │ │ │ │ +[1] 30004 1953 │ │ │ │ │ │ │ │ │ │ $variables$isSymbolic │ │ │ │ │ -[1] 31801 1773 │ │ │ │ │ +[1] 32264 1787 │ │ │ │ │ │ │ │ │ │ $variables$numtDetect │ │ │ │ │ -[1] 33866 1561 │ │ │ │ │ +[1] 34357 1573 │ │ │ │ │ │ │ │ │ │ $variables$pairs2breakpointgr │ │ │ │ │ -[1] 35726 2723 │ │ │ │ │ +[1] 36243 2737 │ │ │ │ │ │ │ │ │ │ $variables$partner │ │ │ │ │ -[1] 38739 1365 │ │ │ │ │ +[1] 39284 1378 │ │ │ │ │ │ │ │ │ │ $variables$rtDetect │ │ │ │ │ -[1] 40394 1377 │ │ │ │ │ +[1] 40967 1390 │ │ │ │ │ │ │ │ │ │ $variables$simpleEventLength │ │ │ │ │ -[1] 42069 767 │ │ │ │ │ +[1] 42671 780 │ │ │ │ │ │ │ │ │ │ $variables$simpleEventType │ │ │ │ │ -[1] 43134 1216 │ │ │ │ │ +[1] 43763 1231 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $references │ │ │ │ │ $references$`env::1` │ │ │ │ │ -[1] 0 294 │ │ │ │ │ +[1] 0 308 │ │ │ │ │ │ │ │ │ │ $references$`env::10` │ │ │ │ │ -[1] 16607 303 │ │ │ │ │ +[1] 16862 317 │ │ │ │ │ │ │ │ │ │ $references$`env::11` │ │ │ │ │ -[1] 18076 301 │ │ │ │ │ +[1] 18359 314 │ │ │ │ │ │ │ │ │ │ $references$`env::12` │ │ │ │ │ -[1] 19605 302 │ │ │ │ │ +[1] 19915 315 │ │ │ │ │ │ │ │ │ │ $references$`env::13` │ │ │ │ │ -[1] 22730 300 │ │ │ │ │ +[1] 23067 314 │ │ │ │ │ │ │ │ │ │ $references$`env::14` │ │ │ │ │ -[1] 24396 299 │ │ │ │ │ +[1] 24760 313 │ │ │ │ │ │ │ │ │ │ $references$`env::15` │ │ │ │ │ -[1] 27630 292 │ │ │ │ │ +[1] 28024 306 │ │ │ │ │ │ │ │ │ │ $references$`env::16` │ │ │ │ │ -[1] 29279 289 │ │ │ │ │ +[1] 29700 304 │ │ │ │ │ │ │ │ │ │ $references$`env::17` │ │ │ │ │ -[1] 31508 293 │ │ │ │ │ +[1] 31957 307 │ │ │ │ │ │ │ │ │ │ $references$`env::18` │ │ │ │ │ -[1] 33574 292 │ │ │ │ │ +[1] 34051 306 │ │ │ │ │ │ │ │ │ │ $references$`env::19` │ │ │ │ │ -[1] 35427 299 │ │ │ │ │ +[1] 35930 313 │ │ │ │ │ │ │ │ │ │ $references$`env::2` │ │ │ │ │ -[1] 1361 298 │ │ │ │ │ +[1] 1388 312 │ │ │ │ │ │ │ │ │ │ $references$`env::20` │ │ │ │ │ -[1] 38449 290 │ │ │ │ │ +[1] 38980 304 │ │ │ │ │ │ │ │ │ │ $references$`env::21` │ │ │ │ │ -[1] 40104 290 │ │ │ │ │ +[1] 40662 305 │ │ │ │ │ │ │ │ │ │ $references$`env::22` │ │ │ │ │ -[1] 41771 298 │ │ │ │ │ +[1] 42357 314 │ │ │ │ │ │ │ │ │ │ $references$`env::23` │ │ │ │ │ -[1] 42836 298 │ │ │ │ │ +[1] 43451 312 │ │ │ │ │ │ │ │ │ │ $references$`env::3` │ │ │ │ │ -[1] 2679 296 │ │ │ │ │ +[1] 2734 310 │ │ │ │ │ │ │ │ │ │ $references$`env::4` │ │ │ │ │ -[1] 4888 303 │ │ │ │ │ +[1] 4971 317 │ │ │ │ │ │ │ │ │ │ $references$`env::5` │ │ │ │ │ -[1] 6212 297 │ │ │ │ │ +[1] 6322 312 │ │ │ │ │ │ │ │ │ │ $references$`env::6` │ │ │ │ │ -[1] 9795 299 │ │ │ │ │ +[1] 9935 312 │ │ │ │ │ │ │ │ │ │ $references$`env::7` │ │ │ │ │ -[1] 11368 303 │ │ │ │ │ +[1] 11537 318 │ │ │ │ │ │ │ │ │ │ $references$`env::8` │ │ │ │ │ -[1] 13237 302 │ │ │ │ │ +[1] 13436 315 │ │ │ │ │ │ │ │ │ │ $references$`env::9` │ │ │ │ │ -[1] 15466 294 │ │ │ │ │ +[1] 15692 310 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $compressed │ │ │ │ │ [1] TRUE │ │ ├── ./usr/lib/R/site-library/StructuralVariantAnnotation/help/paths.rds │ │ │ ├── paths.rds-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,25 +1,25 @@ │ │ │ │ │ - [1] "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/StructuralVariantAnnotation.Rd" │ │ │ │ │ - [2] "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/align_breakpoints.Rd" │ │ │ │ │ - [3] "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/breakendRanges.Rd" │ │ │ │ │ - [4] "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/breakpointGRangesToVCF.Rd" │ │ │ │ │ - [5] "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/breakpointRanges.Rd" │ │ │ │ │ - [6] "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/breakpointgr2bedpe.Rd" │ │ │ │ │ - [7] "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/calculateReferenceHomology.Rd" │ │ │ │ │ - [8] "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/countBreakpointOverlaps.Rd" │ │ │ │ │ - [9] "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/elementExtract.Rd" │ │ │ │ │ -[10] "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/extractBreakpointSequence.Rd" │ │ │ │ │ -[11] "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/extractReferenceSequence.Rd" │ │ │ │ │ -[12] "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/findBreakpointOverlaps.Rd" │ │ │ │ │ -[13] "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/findInsDupOverlaps.Rd" │ │ │ │ │ -[14] "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/findTransitiveCalls.Rd" │ │ │ │ │ -[15] "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/hasPartner.Rd" │ │ │ │ │ -[16] "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/isStructural.Rd" │ │ │ │ │ -[17] "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/isSymbolic.Rd" │ │ │ │ │ -[18] "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/numtDetect.Rd" │ │ │ │ │ -[19] "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/pairs2breakpointgr.Rd" │ │ │ │ │ -[20] "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/partner.Rd" │ │ │ │ │ -[21] "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/rtDetect.Rd" │ │ │ │ │ -[22] "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/simpleEventLength.Rd" │ │ │ │ │ -[23] "/home/moeller/Salsa/r-bioc-structuralvariantannotation/man/simpleEventType.Rd" │ │ │ │ │ + [1] "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/StructuralVariantAnnotation.Rd" │ │ │ │ │ + [2] "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/align_breakpoints.Rd" │ │ │ │ │ + [3] "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/breakendRanges.Rd" │ │ │ │ │ + [4] "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/breakpointGRangesToVCF.Rd" │ │ │ │ │ + [5] "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/breakpointRanges.Rd" │ │ │ │ │ + [6] "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/breakpointgr2bedpe.Rd" │ │ │ │ │ + [7] "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/calculateReferenceHomology.Rd" │ │ │ │ │ + [8] "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/countBreakpointOverlaps.Rd" │ │ │ │ │ + [9] "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/elementExtract.Rd" │ │ │ │ │ +[10] "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/extractBreakpointSequence.Rd" │ │ │ │ │ +[11] "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/extractReferenceSequence.Rd" │ │ │ │ │ +[12] "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/findBreakpointOverlaps.Rd" │ │ │ │ │ +[13] "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/findInsDupOverlaps.Rd" │ │ │ │ │ +[14] "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/findTransitiveCalls.Rd" │ │ │ │ │ +[15] "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/hasPartner.Rd" │ │ │ │ │ +[16] "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/isStructural.Rd" │ │ │ │ │ +[17] "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/isSymbolic.Rd" │ │ │ │ │ +[18] "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/numtDetect.Rd" │ │ │ │ │ +[19] "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/pairs2breakpointgr.Rd" │ │ │ │ │ +[20] "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/partner.Rd" │ │ │ │ │ +[21] "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/rtDetect.Rd" │ │ │ │ │ +[22] "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/simpleEventLength.Rd" │ │ │ │ │ +[23] "/build/reproducible-path/r-bioc-structuralvariantannotation-1.28.0+ds/man/simpleEventType.Rd" │ │ │ │ │ attr(,"first") │ │ │ │ │ -[1] 60 │ │ │ │ │ +[1] 75