Merge branch 'release/v2.0.2'

Patch fixing PS tag

Author: ACEnglish

Cargo.lock

@@ -1,6 +1,6 @@
 [package]
 name = "kanpig"
-version = "2.0.1"
+version = "2.0.2"
 edition = "2021"
 
 [dependencies]

Cargo.toml

@@ -6,6 +6,7 @@ TESTS=(
     "plat"
     "mims"
     "pybind"
+    "ps_test"
 )
 
 # Run from truvari's base directory

repo_utils/kanpig_tests.sh

@@ -0,0 +1,21 @@
+OD=$1
+SRC=$2
+
+$kanpig gt \
+    --reads ${SRC}/HG002_withHP.plup.gz \
+    --input ${SRC}/baseline.vcf.gz \
+    --reference ${REF} \
+    -o ${OD}/with.vcf
+
+result=$(bcftools query -f "[%PS]\n" ${OD}/with.vcf)
+test "$result" = "8903002" || exit 1
+
+
+$kanpig gt \
+    --reads ${SRC}/HG002_woHP.plup.gz \
+    --input ${SRC}/baseline.vcf.gz \
+    --reference ${REF} \
+    -o ${OD}/without.vcf
+
+result=$(bcftools query -f "[%PS]\n" ${OD}/without.vcf)
+test "$result" = "9015824" || exit 1

repo_utils/ps_test/HG002_withHP.plup.gz

@@ -285,8 +285,8 @@ fn finalize_annotation(
     // Either use haplotagging PS or NE (+1 for 1-based like in the VCF)
     let ps = paths
         .first()
-        .and_then(|p| p.meta.ps.get(sample_idx).copied())
-        .unwrap_or(Some((neigh_group + 1) as u32));
+        .and_then(|p| p.meta.ps.get(sample_idx).and_then(|&ps| ps))
+        .or(Some((neigh_group + 1) as u32));
 
     let ad = vec![Some(ref_cov as i32), Some((alt_cov1 + alt_cov2) as i32)];