Fix regex counting of tabs in read_report (fixes #74)

fbreitwieser · Apr 13, 2021 · 8dd99bb · 8dd99bb
1 parent 5f05969
commit 8dd99bb
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Showing 14 changed files with 96 additions and 37 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: pavian
 Type: Package
 Title: Visualize and analyze metagenomics classification results
-Version: 1.0.0
+Version: 1.1.0
 URL: https://github.com/fbreitwieser/pavian
 BugReports: https://github.com/fbreitwieser/pavian/issues
 Authors@R: person("Florian P", "Breitwieser", email = "[email protected]", role = c("aut", "cre"))
@@ -20,6 +20,6 @@ Remotes: github::fbreitwieser/sankeyD3,
         github::fbreitwieser/shinyFileTree
 License: GPL-3
 LazyData: TRUE
-RoxygenNote: 6.1.1
+RoxygenNote: 7.1.0
 VignetteBuilder: knitr
 NeedsCompilation: no
diff --git a/R/datainput-read_report.R b/R/datainput-read_report.R
@@ -395,7 +395,9 @@ read_report <- function(myfile, has_header=NULL, check_file = FALSE) {
   is_metaphlan_fmt <- grepl("Metaphlan2_Analysis$", first.line)
   is_krakenu_fmt <- grepl("^.?%\treads\ttaxReads\tkmers", first.line)
   is_kaiju_fmt <- grepl("^  *%\t  *reads", first.line)
-  ntabs <- as.numeric(regexpr('\t', first.line))
+
+  ntabs <- lengths(regmatches(first.line, gregexpr("\t", first.line)))
+
   nrows <- ifelse(isTRUE(check_file), 5, -1)
   if (!is_krakenu_fmt && is_kaiju_fmt) {
     cont <- readLines(myfile)

diff --git a/man/comparisonModule.Rd b/man/comparisonModule.Rd
diff --git a/man/dataInputModule.Rd b/man/dataInputModule.Rd
diff --git a/man/dataInputModuleUI.Rd b/man/dataInputModuleUI.Rd
diff --git a/man/filter_taxa.Rd b/man/filter_taxa.Rd
diff --git a/man/merge_reports2.Rd b/man/merge_reports2.Rd
diff --git a/man/read_report2.Rd b/man/read_report2.Rd
diff --git a/man/read_sample_data.Rd b/man/read_sample_data.Rd
diff --git a/man/read_server_directory1.Rd b/man/read_server_directory1.Rd
diff --git a/man/reportOverviewModule.Rd b/man/reportOverviewModule.Rd
diff --git a/man/runApp.Rd b/man/runApp.Rd
diff --git a/man/sampleModule.Rd b/man/sampleModule.Rd
diff --git a/tests/testthat/read_report/ref_output/k2uniq-report-res.rds b/tests/testthat/read_report/ref_output/k2uniq-report-res.rds