fix: expand() converts Number=A to Number=1 in headers (#79)

DESCRIPTION

@@ -3,7 +3,7 @@ Type: Package
 Title: Annotation of Genetic Variants
 Description: Annotate variants, compute amino acid coding changes,
         predict coding outcomes.
-Version: 1.59.0
+Version: 1.59.1
 Authors@R: c(
         person("Valerie", "Oberchain", role="aut"),
         person("Martin", "Morgan", role="aut"),

NEWS

@@ -1,3 +1,16 @@
+CHANGES IN VERSION 1.59.1
+-------------------------
+
+BUG FIXES
+
+    o expand() now converts Number=A to Number=1 in both INFO and FORMAT
+      VCF header metadata. After expansion, each row contains exactly one
+      ALT allele, so per-ALT fields are scalar. This fixes the round-trip
+      discrepancy where writeVcf() followed by readVcf() + expand() would
+      produce a CompressedNumericList for fields like AF instead of a plain
+      numeric vector. The fix applies to both the multi-allele expansion
+      path and the biallelic early-return path. (GitHub issue #79)
+
 CHANGES IN VERSION 1.36.0
 -------------------------
 

R/methods-expand.R

@@ -13,17 +13,18 @@ setMethod("expand", "CollapsedVCF",
         if (all(elt == 1L)) {
             fxd <- fixed(x)
             fxd$ALT <- unlist(alt(x), use.names=FALSE)
-			ghdr <- geno(header(x))
-			varsR <- rownames(ghdr)[rownames(ghdr) == "AD" | ghdr$Number == "R"]
-			varsR <- varsR[varsR %in% names(geno(x))]
-			if (length(varsR) > 0){
-				geno(x)[varsR] <- endoapply(
-					geno(x)[varsR], function(i)
-						.expandAD(i, nrow(x), ncol(x))
-				)
-			}
-            return(VCF(rd, colData(x), metadata(x), fxd, .unlistAltInfo(x), 
-                       geno(x), ..., collapsed=FALSE))
+            ghdr <- geno(header(x))
+            varsR <- rownames(ghdr)[rownames(ghdr) == "AD" | ghdr$Number == "R"]
+            varsR <- varsR[varsR %in% names(geno(x))]
+            if (length(varsR) > 0){
+                geno(x)[varsR] <- endoapply(
+                    geno(x)[varsR], function(i)
+                        .expandAD(i, nrow(x), ncol(x))
+                )
+            }
+            res <- VCF(rd, colData(x), metadata(x), fxd, .unlistAltInfo(x),
+                       geno(x), ..., collapsed=FALSE)
+            return(.updateHeaderNumberA(res))
         }
 
         ## info, fixed, geno
@@ -40,17 +41,36 @@ setMethod("expand", "CollapsedVCF",
             mcols(rdexp) <- NULL
         } else rdexp <- rd[idx, "paramRangeID"]
 
-        tmp = VCF(rdexp, colData(x), metadata(x), fexp, iexp, gexp,
-            ..., collapsed=FALSE)  # https://github.com/Bioconductor/VariantAnnotation/issues/79 says 'A' should not occur in info(header())$Number
-        nhi = info(header(tmp))
-        num = nhi$Number
-        inda = grep("A", num)
-        if (length(inda)>0) num[inda] = "1"
-        info(header(tmp))$Number = num
-        tmp
+        res <- VCF(rdexp, colData(x), metadata(x), fexp, iexp, gexp,
+            ..., collapsed=FALSE)
+        .updateHeaderNumberA(res)
     }
 )
 
+## After expand(), each row has exactly one ALT allele, so per-ALT fields
+## (Number=A) are now scalar — update the header to reflect this.
+## (GitHub issue #79)
+.updateHeaderNumberA <- function(vcf)
+{
+    ## INFO header
+    ihdr <- info(header(vcf))
+    if (nrow(ihdr) > 0L) {
+        isA <- ihdr$Number == "A"
+        if (any(isA))
+            ihdr$Number[isA] <- "1"
+        info(header(vcf)) <- ihdr
+    }
+    ## FORMAT/geno header
+    ghdr <- geno(header(vcf))
+    if (nrow(ghdr) > 0L) {
+        isA <- ghdr$Number == "A"
+        if (any(isA))
+            ghdr$Number[isA] <- "1"
+        geno(header(vcf)) <- ghdr
+    }
+    vcf
+}
+
 .expandGeno <- function(x, hdr, elt, idx)
 {
     gvar <- geno(x)

inst/unitTests/test_expand-methods.R

@@ -90,3 +90,37 @@ test_expand_adr_adf <- function()
 			})
 
 }
+
+## ---------------------------------------------------------------
+## Test for GitHub issue #79: Number=A should become Number=1 in
+## both INFO and FORMAT headers after expand().
+## ---------------------------------------------------------------
+test_expand_numberA_to_1_issue79 <- function()
+{
+    ## Test with multi-allele VCF (exercises main expand path)
+    fl <- system.file("unitTests", "cases", "expand.vcf",
+                      package="VariantAnnotation")
+    vcf <- suppressWarnings(readVcf(fl, "hg19"))
+    checkIdentical(info(header(vcf))["AF", "Number"], "A")
+    exp <- expand(vcf)
+    checkIdentical(info(header(exp))["AF", "Number"], "1")
+    checkTrue(is.numeric(info(exp)$AF))
+
+    ## Test with biallelic VCF (exercises early-return path)
+    fl2 <- system.file("extdata", "ex2.vcf", package="VariantAnnotation")
+    vcf2 <- readVcf(fl2)
+    checkIdentical(info(header(vcf2))["AF", "Number"], "A")
+    exp2 <- expand(vcf2)
+    checkIdentical(info(header(exp2))["AF", "Number"], "1")
+    checkTrue(is.numeric(info(exp2)$AF))
+
+    ## Round-trip: writeVcf + readVcf + expand should keep AF as numeric
+    out <- tempfile(fileext=".vcf")
+    on.exit(unlink(out))
+    writeVcf(exp2, out)
+    rt <- readVcf(out, row.names=FALSE)
+    rt <- expand(rt)
+    checkIdentical(info(header(rt))["AF", "Number"], "1")
+    checkTrue(is.numeric(info(rt)$AF))
+    checkEquals(info(exp2)$AF, info(rt)$AF)
+}