From 3d1a308e1bbe3bb8e126ca78c16012959616d4d0 Mon Sep 17 00:00:00 2001
From: John Muirhead-Gould <john@magna-services.com>
Date: Wed, 1 Jul 2026 19:41:49 -0400
Subject: [PATCH] fix: preserve '*' spanning deletion alleles at read time
 (#65)
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VCFs containing '*' (spanning deletion) alleles are now read with a
CharacterList ALT column, preserving the '*' character. Previously,
.formatALT() converted '*' to an empty string to fit into DNAStringSet,
but this made it impossible to write valid VCF output — IGV/htsjdk
would reject files with empty alleles.

The fix treats '*' as a structural/special allele (like '<DEL>'), which
causes .isStructural() to return TRUE and the ALT to be stored as a
CharacterList. This is semantically correct per the VCF spec: '*'
represents a spanning deletion and is not a DNA sequence.

For VCFs without '*' alleles, behavior is unchanged (DNAStringSetList).

This supersedes the write-path-only fix in PR #103, which could only
handle the multi-allele case. With this read-time fix, both single '*'
and multi-allele '*' are correctly round-tripped.

Closes #65
---
 DESCRIPTION      |  2 +-
 NEWS             | 15 +++++++++++++++
 R/AllUtilities.R |  6 ++++--
 3 files changed, 20 insertions(+), 3 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 9bdc489..7967a72 100644
--- a/DESCRIPTION
+++ b/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"),
diff --git a/NEWS b/NEWS
index 6fcc401..ce2e22f 100644
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,18 @@
+CHANGES IN VERSION 1.59.1
+-------------------------
+
+BUG FIXES
+
+    o readVcf() now preserves '*' (spanning deletion) alleles instead of
+      converting them to empty strings. VCFs containing '*' alleles are
+      returned with a CharacterList ALT column (same as structural variant
+      VCFs), allowing faithful round-trip through writeVcf(). Previously,
+      '*' was erased at read time making it impossible to write valid VCF
+      output for files containing spanning deletions — IGV/htsjdk would
+      reject the output with "empty alleles are not permitted". VCFs
+      without '*' alleles continue to use DNAStringSetList as before.
+      (GitHub issue #65)
+
 CHANGES IN VERSION 1.36.0
 -------------------------
 
diff --git a/R/AllUtilities.R b/R/AllUtilities.R
index e0478c2..bd7485b 100644
--- a/R/AllUtilities.R
+++ b/R/AllUtilities.R
@@ -110,7 +110,6 @@
         CharacterList(x)
     } else {
         flat[grepl("I", flat, fixed=TRUE)] <- "."
-        flat[grepl("*", flat, fixed=TRUE)] <- "" 
         relist(DNAStringSet(flat), x)
     }
 }
@@ -118,12 +117,15 @@
 ## The grep for '.' here is looking for '.' as *part* of the ALT field.
 ## If the ALT were '.' only, with no other characters, it would have been
 ## converted to an empty string in the C code before it reached this point.
+## '*' is the VCF spanning deletion allele — not valid DNA, treated as
+## structural so it's preserved in a CharacterList (GitHub issue #65).
 .isStructural <- function(x)
 {
     grepl("<", x, fixed=TRUE) |
     grepl("[", x, fixed=TRUE) |
     grepl("]", x, fixed=TRUE) |
-    grepl(".", x, fixed=TRUE)
+    grepl(".", x, fixed=TRUE) |
+    grepl("*", x, fixed=TRUE)
 }
 
 .formatInfo <- function(x, hdr, nrecords)