fix: writeVcf preserves fileDate and suppresses bare contig lines (#78)

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 +1,21 @@
+CHANGES IN VERSION 1.59.1
+-------------------------
+
+BUG FIXES
+
+    o writeVcf() now preserves the existing fileDate header value instead
+      of unconditionally replacing it with the current date. This restores
+      provenance information and enables faithful round-trips.
+
+    o writeVcf() no longer emits bare ##contig=<ID=X> header lines when
+      seqinfo contains only NA seqlengths and NA genomes. Such lines are
+      uninformative and were the primary cause of round-trip mismatches
+      (extra contig lines altered the header structure on re-read).
+
+    o Together these changes allow all.equal(readVcf(writeVcf(x)), x)
+      to succeed for VCFs whose seqinfo is all-NA (e.g., structural.vcf).
+      (GitHub issue #78)
+
 CHANGES IN VERSION 1.36.0
 -------------------------
 

R/methods-writeVcf.R

@@ -152,8 +152,15 @@
         header <- c(fileformat, header) 
     }
     contig <- any(grepl("contig", names(header), fixed=TRUE))
-    if (!contig)
-        header <- c(header, .contigsFromSeqinfo(seqinfo(obj)))
+    if (!contig) {
+        ## Only add contig lines if seqinfo carries useful information
+        ## (at least one non-NA seqlength or genome). Bare ##contig=<ID=X>
+        ## lines are uninformative and break round-trip fidelity (#78).
+        si <- seqinfo(obj)
+        has_info <- !all(is.na(seqlengths(si))) || !all(is.na(genome(si)))
+        if (has_info)
+            header <- c(header, .contigsFromSeqinfo(si))
+    }
 
     ## Last line before data
     colnms <- c("#CHROM", "POS", "ID", "REF", "ALT", "QUAL", "FILTER", "INFO")
@@ -171,11 +178,12 @@
     if (nms == "META" && ncol(df) == 1L) {
         if (!"fileformat" %in% rownames(df))
             df <- rbind(DataFrame(Value="VCFv4.3", row.names="fileformat"), df)
-        fd <- format(Sys.time(), "%Y%m%d")
-        if ("fileDate" %in% rownames(df))
-            df[rownames(df) == "fileDate", ] <- fd
-        else
+        ## Preserve existing fileDate for round-trip fidelity (#78).
+        ## Only add a new fileDate if none exists.
+        if (!"fileDate" %in% rownames(df)) {
+            fd <- format(Sys.time(), "%Y%m%d")
             df <- rbind(df, DataFrame(Value=fd, row.names="fileDate"))
+        }
         paste("##", rownames(df), "=", df[,1], sep="")
     ## Support VCF v4.2 and v4.3 PEDIGREE field
     } else if(nms == "PEDIGREE" || nms == "ALT") {
@@ -193,8 +201,8 @@
     ## (Rsamtools reports unstructured headers as one column named "Value")
     } else if(ncol(df) == 1L && names(df)[1] == "Value" && nrow(df) == 1L) {
         if (nms == "fileDate") {
-            fd <- format(Sys.time(), "%Y%m%d")
-            paste("##fileDate=", fd, sep="")
+            ## Preserve existing fileDate for round-trip fidelity (#78).
+            paste("##fileDate=", df[1, 1], sep="")
         } else
             paste("##", nms, "=", df[,1], sep="")
     ## 'non-simple' key-value pairs

inst/unitTests/test_writeVcf-methods.R

@@ -133,3 +133,38 @@ chk = fixed(header(readVcf(tmp)))$ALT
 checkIdentical(chk, good)
 }
 
+
+## ---------------------------------------------------------------
+## Test for GitHub issue #78: faithful round-trip via writeVcf + readVcf
+## ---------------------------------------------------------------
+test_writeVcf_roundtrip_issue78 <- function()
+{
+    ## structural.vcf has all-NA seqinfo and an existing fileDate
+    fl <- system.file("extdata", "structural.vcf", package="VariantAnnotation")
+    out <- tempfile(fileext=".vcf")
+    on.exit(unlink(out))
+
+    first <- readVcf(fl)
+    writeVcf(first, out)
+    roundtrip <- readVcf(out)
+
+    ## Should be identical (no spurious contig lines, fileDate preserved)
+    checkTrue(isTRUE(all.equal(roundtrip, first)),
+        msg="structural.vcf round-trip should be perfect")
+
+    ## ex2.vcf has real seqinfo — contig lines should still be written
+    fl2 <- system.file("extdata", "ex2.vcf", package="VariantAnnotation")
+    out2 <- tempfile(fileext=".vcf")
+    on.exit(unlink(out2), add=TRUE)
+
+    first2 <- readVcf(fl2)
+    writeVcf(first2, out2)
+    roundtrip2 <- readVcf(out2)
+    checkTrue(isTRUE(all.equal(roundtrip2, first2)),
+        msg="ex2.vcf round-trip should be perfect")
+
+    ## Verify fileDate is preserved (not replaced with today's date)
+    lines <- readLines(out2)
+    fd_line <- grep("^##fileDate=", lines, value=TRUE)
+    checkIdentical(fd_line, "##fileDate=20090805")
+}