diff --git a/CHANGES.md b/CHANGES.md
index b9b2262..8db6631 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -3,6 +3,7 @@ v0.1.3
 + exit with error on multi-allelics (previously, only first allele was used) ( #11)
 + more docs on conf file (thanks @m-pauper)
 + fix compression error for very dense regions (#12)
++ fix error when using hts_set_threads more than once and after reading header (#12)
 
 v0.1.2
 ======
diff --git a/Cargo.toml b/Cargo.toml
index d841408..7b60b8e 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -18,7 +18,7 @@ path = "src/main.rs"
 
 flate2 = { version = "1.0", features = ["zlib-ng-compat"]}
 
-rust-htslib = { version = "*", features = ["libdeflate", "static"] }
+rust-htslib = { version = "0.38.2", features = ["libdeflate", "static"] }
 #bitpacking = "0.8.4"
 stream-vbyte = {version = "0.4.0", features=["x86_ssse3", "x86_sse41"]}
 clap = {version = "~2.27.0", features=["suggestions"] }
diff --git a/src/commands/encoder_cmd.rs b/src/commands/encoder_cmd.rs
index cee280f..cd59de6 100644
--- a/src/commands/encoder_cmd.rs
+++ b/src/commands/encoder_cmd.rs
@@ -261,9 +261,9 @@ pub fn encoder_main(vpaths: Vec<&str>, opath: &str, jpath: &str) {
                     Err(error) => panic!("problem opening from stdin: {:?}", error),
                 }
             };
+            vcf.set_threads(2).ok();
         }
         eprintln!("[echtvar] adding VCF:{}", vpath);
-        vcf.set_threads(2).ok();
 
         for r in vcf.records() {
             let rec = r.expect("error getting record");
@@ -377,7 +377,7 @@ pub fn encoder_main(vpaths: Vec<&str>, opath: &str, jpath: &str) {
             }
 
             let alleles = rec.alleles();
-            if alleles.len() > 2 {
+            if alleles.len() != 2 {
                 panic!(
                     "[echtvar] variants must be decomposed before running {:?}",
                     rec
diff --git a/src/lib/echtvar.rs b/src/lib/echtvar.rs
index 20f76b1..6fe92ab 100644
--- a/src/lib/echtvar.rs
+++ b/src/lib/echtvar.rs
@@ -339,7 +339,7 @@ impl EchtVars {
         }
 
         let alleles = variant.alleles();
-        if alleles.len() > 2 {
+        if alleles.len() != 2 {
             panic!(
                 "[echtvar] variants must be decomposed before running. got variant with {} alleles at {}:{}",
                 alleles.len() - 1,