From f0017e420481238ca0386dced72e90ae00bfa70b Mon Sep 17 00:00:00 2001
From: Brent Pedersen <bpederse@gmail.com>
Date: Tue, 15 Mar 2022 15:37:28 +0100
Subject: [PATCH] pre-allocate variable vectors for fasteval so they don't move

this was causing bugs where the expression values were not filled
correctly for each variant because the addresses were changed.
---
 CHANGES.md                   | 4 ++++
 Cargo.toml                   | 2 +-
 src/commands/annotate_cmd.rs | 4 ++--
 src/lib/echtvar.rs           | 5 +++--
 4 files changed, 10 insertions(+), 5 deletions(-)

diff --git a/CHANGES.md b/CHANGES.md
index 8db6631..8f24814 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -1,3 +1,7 @@
+v0.1.4
+======
++ fix bug with filter not removing (not filtering) variants correctly.
+
 v0.1.3
 ======
 + exit with error on multi-allelics (previously, only first allele was used) ( #11)
diff --git a/Cargo.toml b/Cargo.toml
index 7b60b8e..69f7988 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "echtvar"
-version = "0.1.3"
+version = "0.1.4"
 edition = "2018"
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
diff --git a/src/commands/annotate_cmd.rs b/src/commands/annotate_cmd.rs
index f3698e7..7c5a911 100644
--- a/src/commands/annotate_cmd.rs
+++ b/src/commands/annotate_cmd.rs
@@ -38,11 +38,11 @@ pub fn annotate_main(
     let parser = fasteval::Parser::new();
     let mut slab = fasteval::Slab::new();
     let mut ns = fasteval::EmptyNamespace;
-    let mut expr_values = vec![];
+    let mut expr_values = Vec::with_capacity(echts.len());
 
     for (i, e) in echts.iter().enumerate() {
         // a vector within expr_values for each echtvar file.
-        expr_values.push(vec![]);
+        expr_values.push(Vec::with_capacity(e.fields.len()));
         // handle the expression stuff.
         for (j, fld) in e.fields.iter().enumerate() {
             expr_values[i].push(0.0 as f64);
diff --git a/src/lib/echtvar.rs b/src/lib/echtvar.rs
index 6fe92ab..6fdb1d1 100644
--- a/src/lib/echtvar.rs
+++ b/src/lib/echtvar.rs
@@ -341,10 +341,11 @@ impl EchtVars {
         let alleles = variant.alleles();
         if alleles.len() != 2 {
             panic!(
-                "[echtvar] variants must be decomposed before running. got variant with {} alleles at {}:{}",
+                "[echtvar] variants must be decomposed before running. got variant with {} alleles at {}:{} ({:?})",
                 alleles.len() - 1,
                 variant.chrom(),
-                variant.position() + 1
+                variant.position() + 1,
+                variant.alleles()
             );
         }
         let eidx = if alleles[0].len() + alleles[1].len() <= crate::var32::MAX_COMBINED_LEN {