Fix crash in haplotyping where there are null v-calls or c-valls with no

* in the name
airr-community · Nov 22, 2024 · 500cc15 · 500cc15
1 parent 8e91247
commit 500cc15
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diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -1,3 +1,3 @@
-Version: 0.5.0
-Date: 2023-03-08 14:31:07 UTC
-SHA: 7be6bb08b96eea277f1900b9b8f74da74136d4dd
+Version: 0.5.2
+Date: 2024-11-02 14:58:37 UTC
+SHA: 8e9124785ceea473dc545641cc9ebf3a13dbedda
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: ogrdbstats
 Type: Package
 Title: Analysis of Adaptive Immune Receptor Repertoire Germ Line Statistics
-Version: 0.5.2
+Version: 0.5.2.1
 Authors@R: person(
   "William", "Lees",
   email = "[email protected]",
@@ -42,5 +42,5 @@ Suggests:
   knitr,
   rmarkdown
 VignetteBuilder: knitr
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 LazyData: true
diff --git a/R/genotype_statistics.R b/R/genotype_statistics.R
@@ -568,7 +568,18 @@ calc_haplo_details = function(segment, input_sequences) {
     sa = rename(sa, A_CALL=V_CALL)
   }
 
-  sa$a_gene = sapply(sa$A_CALL, function(x) {strsplit(x, '*', fixed=TRUE)[[1]][[1]]})
+  sa$a_gene = sapply(sa$A_CALL, function(x) {
+      if (grepl('*', x, fixed=TRUE)) {
+        strsplit(x, '*', fixed=TRUE)[[1]][[1]]
+      } else {
+        'X'
+      }
+    })
+
+  if (nrow(sa) == 0) {
+    return(list())
+  }
+
   sa$a_allele = sapply(sa$A_CALL, function(x) {
       if (grepl('*', x, fixed=TRUE)) {
         strsplit(x, '*', fixed=TRUE)[[1]][[2]]

diff --git a/cran-comments.md b/cran-comments.md
@@ -3,6 +3,6 @@
 0 errors | 0 warnings | 0 notes
 
 
-This is a minor update to resolve a problem notified by CRAN Package Check : https://cran.r-project.org/web/checks/check_results_ogrdbstats.html
+This is a patch to resolve a problem notified by CRAN Package Check : https://cran.r-project.org/web/checks/check_results_ogrdbstats.html
 
 I reproduced and fixed the problem. Have tested on windows, ubuntu and macos - latest, ubuntu-latest devel.
diff --git a/vignettes/man/figures/README-unnamed-chunk-1-1.png b/vignettes/man/figures/README-unnamed-chunk-1-1.png
diff --git a/vignettes/using_ogrdbstats.R b/vignettes/using_ogrdbstats.R
@@ -23,7 +23,7 @@ rd = suppressMessages(
 barplot_grobs = make_barplot_grobs(rd$input_sequences, rd$genotype_db, rd$inferred_seqs, 
                                    rd$genotype, 'V', rd$calculated_NC)
 base_grobs = make_novel_base_grobs(rd$inferred_seqs, rd$input_sequences, 'V', FALSE)
-gridExtra::grid.arrange(grobs=list(barplot_grobs[3][[1]], base_grobs$end[1][[1]], 
+gridExtra::grid.arrange(grobs=list(barplot_grobs[2][[1]], base_grobs$end[1][[1]], 
                                    base_grobs$conc[1][[1]]),ncol=1)
 
 

diff --git a/vignettes/using_ogrdbstats.html b/vignettes/using_ogrdbstats.html
diff --git a/vignettes/using_ogrdbstats.md b/vignettes/using_ogrdbstats.md
@@ -1,7 +1,7 @@
 Using ogrdbstats
 ================
 William Lees
-2023-03-08
+2024-11-22
 
 # Conducting a Genotype Analysis with ogrdbstats
 
@@ -368,7 +368,7 @@ rd = suppressMessages(
 barplot_grobs = make_barplot_grobs(rd$input_sequences, rd$genotype_db, rd$inferred_seqs, 
                                    rd$genotype, 'V', rd$calculated_NC)
 base_grobs = make_novel_base_grobs(rd$inferred_seqs, rd$input_sequences, 'V', FALSE)
-gridExtra::grid.arrange(grobs=list(barplot_grobs[3][[1]], base_grobs$end[1][[1]], 
+gridExtra::grid.arrange(grobs=list(barplot_grobs[2][[1]], base_grobs$end[1][[1]], 
                                    base_grobs$conc[1][[1]]),ncol=1)
 ```