Throw error in index_snps() if map has missing values (Issue rqtl#218)

kbroman · Apr 5, 2024 · 10a5e16 · 10a5e16
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: qtl2
-Version: 0.35-1
-Date: 2024-03-15
+Version: 0.35-2
+Date: 2024-04-05
 Title: Quantitative Trait Locus Mapping in Experimental Crosses
 Description: Provides a set of tools to perform quantitative
     trait locus (QTL) analysis in experimental crosses. It is a

diff --git a/NEWS.md b/NEWS.md
@@ -1,9 +1,12 @@
-## qtl2 0.35-1 (2024-03-15)
+## qtl2 0.35-2 (2024-04-05)
 
 ### Bug fixes
 
 - Fixed a problem with `sdp_panel=TRUE` in `plot_snpasso()`. (Issue #232)
 
+- Stop `index_snps()` with an error if physical map has missing
+  values. (Issue #218)
+
 
 ## qtl2 0.34 (2023-11-28)
 

diff --git a/R/index_snps.R b/R/index_snps.R
@@ -114,6 +114,7 @@ index_snps <-
 
     ### find snps in map
     this_map <- map[[uchr]]
+    if(any(is.na(this_map))) stop("Missing values in map on chr ", uchr)
     snploc <- find_intervals(snpinfo$pos, this_map, tol)
     interval <- snploc[,1]
     on_map <- (snploc[,2]==1)