From 842443d8379ea1baeee55a2553df52423c038c58 Mon Sep 17 00:00:00 2001 From: Changqing Wang Date: Mon, 8 Apr 2024 16:58:55 +1000 Subject: [PATCH] #29: update minimap2 and samtools versions; #27 --- DESCRIPTION | 2 +- R/minimap2_align.R | 4 +++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index fb0aa60..e28bc02 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -87,7 +87,7 @@ Suggests: testthat (>= 3.0.0), xml2 LinkingTo: Rcpp, Rhtslib, zlibbioc, testthat -SystemRequirements: GNU make, C++17, samtools (>= 1.14), minimap2 (>= 2.28) +SystemRequirements: GNU make, C++17, samtools (>= 1.19), minimap2 (>= 2.17) RoxygenNote: 7.3.1 VignetteBuilder: knitr URL: https://github.com/OliverVoogd/FLAMES diff --git a/R/minimap2_align.R b/R/minimap2_align.R index 2ad3059..9c2fb22 100755 --- a/R/minimap2_align.R +++ b/R/minimap2_align.R @@ -79,7 +79,9 @@ minimap2_align <- function(config, fa_file, fq_in, annot, outdir, minimap2 = NA, ">", file.path(outdir, "tmp_splice_anno.bed12"))) if (!is.null(base::attr(paftoolsjs_status, "status")) && base::attr(paftoolsjs_status, "status") != 0) { - stop(paste0("error running k8 paftools.js gff2bed:\n", paftoolsjs_status)) + stop(paste0("error running k8 paftools.js gff2bed:\n", paftoolsjs_status, "\n", + "Are you using NCBI GFF3? It is not well supported by minimap2's paftools.js")) + )) } minimap2_args <- base::append(minimap2_args, c("--junc-bed", file.path(outdir, "tmp_splice_anno.bed12"), "--junc-bonus", "1"))