don't use set_threads after reading header

found with test-file from #12

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"] }

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

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,