Rsamtools / rtracklayer creating csi index for BAM files
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ATpoint ★ 3.6k
Last seen 21 hours ago

I am asking this out of personal interest based on this Biostars post where OP aimed to export a BAM file with long chromosomes that do not fit into the default bai index, resulting in the error message one can see in that post.

export(anyBamfile.bam, BamFile(file = "exported.bam"))

After digging in the source code a bit the best I came up with was deactivating the indexing via index = FALSE and do it manually via samtools, but there must be a way to do it. Maybe an auto-detect option to build csi index automatically instead of bai if contig length exceeds the maximum of bai would be a good addition.

R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.5

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] rtracklayer_1.44.2          GenomicAlignments_1.20.1    Rsamtools_2.0.0             Biostrings_2.52.0           XVector_0.24.0              DESeq2_1.24.0               statmod_1.4.32             
 [8] csaw_1.18.0                 tximport_1.12.3             data.table_1.12.2           edgeR_3.26.5                limma_3.40.6                zinbwave_1.6.0              SingleCellExperiment_1.6.0 
[15] SummarizedExperiment_1.14.0 DelayedArray_0.10.0         BiocParallel_1.18.0         matrixStats_0.54.0          Biobase_2.44.0              GenomicRanges_1.36.0        GenomeInfoDb_1.20.0        
[22] IRanges_2.18.1              S4Vectors_0.22.0            BiocGenerics_0.30.0        

loaded via a namespace (and not attached):
 [1] bitops_1.0-6           bit64_0.9-7            RColorBrewer_1.1-2     progress_1.2.2         httr_1.4.0             numDeriv_2016.8-1.1    tools_3.6.1            backports_1.1.4       
 [9] R6_2.4.0               KernSmooth_2.23-15     rpart_4.1-15           Hmisc_4.2-0            DBI_1.0.0              lazyeval_0.2.2         colorspace_1.4-1       nnet_7.3-12           
[17] gridExtra_2.3          tidyselect_0.2.5       prettyunits_1.0.2      bit_1.1-14             compiler_3.6.1         glmnet_3.0-1           pspline_1.0-18         htmlTable_1.13.1      
[25] labeling_0.3           checkmate_1.9.4        scales_1.0.0           mvtnorm_1.0-11         readr_1.3.1            genefilter_1.66.0      stringr_1.4.0          digest_0.6.20         
[33] foreign_0.8-71         htmltools_0.3.6        base64enc_0.1-3        pkgconfig_2.0.2        stabledist_0.7-1       ADGofTest_0.3          htmlwidgets_1.3        rlang_0.4.0           
[41] rstudioapi_0.10        RSQLite_2.1.2          shape_1.4.4            jsonlite_1.6           acepack_1.4.1          dplyr_0.8.3            RCurl_1.95-4.12        magrittr_1.5          
[49] GenomeInfoDbData_1.2.1 Formula_1.2-3          Matrix_1.2-17          Rcpp_1.0.2             munsell_0.5.0          stringi_1.4.3          zlibbioc_1.30.0        grid_3.6.1            
[57] blob_1.2.0             crayon_1.3.4           lattice_0.20-38        splines_3.6.1          GenomicFeatures_1.36.4 annotate_1.62.0        hms_0.5.0              locfit_1.5-9.1        
[65] knitr_1.23             zeallot_0.1.0          pillar_1.4.2           softImpute_1.4         geneplotter_1.62.0     codetools_0.2-16       biomaRt_2.40.3         XML_3.98-1.20         
[73] glue_1.3.1             latticeExtra_0.6-28    BiocManager_1.30.4     vctrs_0.2.0            foreach_1.4.7          gtable_0.3.0           purrr_0.3.2            assertthat_0.2.1      
[81] ggplot2_3.2.0          xfun_0.8               xtable_1.8-4           survival_2.44-1.1      pcaPP_1.9-73           gsl_2.1-6              tibble_2.1.3           copula_0.999-19.1     
[89] iterators_1.0.12       AnnotationDbi_1.46.0   memoise_1.1.0          cluster_2.1.0
rsamtools rtracklayer • 973 views

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