adding tests

ACEnglish · Jan 6, 2024 · 3d4bffa · 3d4bffa
1 parent d79bae2
commit 3d4bffa
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Showing 3 changed files with 19 additions and 3 deletions.
diff --git a/repo_utils/answer_key/phab/phab_result_poa.vcf.gz b/repo_utils/answer_key/phab/phab_result_poa.vcf.gz
diff --git a/repo_utils/sub_tests/phab.sh b/repo_utils/sub_tests/phab.sh
@@ -22,6 +22,17 @@ if [ $test_phab_wfa ]; then
     assert_equal $(fn_md5 $ANSDIR/phab/phab_result_wfa.vcf.gz) $(fn_md5 $OD/phab_result_wfa.vcf.gz)
 fi
 
+run test_phab_poa $truv phab -o $OD/phab_result_poa.vcf.gz \
+                         -b $INDIR/variants/phab_base.vcf.gz \
+                         -c $INDIR/variants/phab_comp.vcf.gz \
+                         -f $INDIR/references/phab_ref.fa \
+                         -r chr1:700-900 --align poa
+if [ $test_phab_poa ]; then
+    assert_exit_code 0
+    assert_equal $(fn_md5 $ANSDIR/phab/phab_result_poa.vcf.gz) $(fn_md5 $OD/phab_result_poa.vcf.gz)
+fi
+
+
 run test_phab_badparams $truv phab -o $OD/phab_result\
     -b doesntexist.vcf \
     -c alsobad.vcf \

diff --git a/truvari/phab.py b/truvari/phab.py
@@ -274,10 +274,15 @@ def poa_to_vars(seq_bytes):
     """
     Run partial order alignment to create msa
     """
-    fasta = {k: v.decode() for k, v in fasta_reader(seq_bytes.decode(), False)}
+    parts = sorted(list(fasta_reader(seq_bytes.decode(), False)))
+    names = []
+    seqs = []
+    for k,v in parts:
+        names.append(k)
+        seqs.append(v.decode().strip())
     aligner = pyabpoa.msa_aligner()
-    aln_result = aligner.msa(fasta.values(), False, True)
-    return truvari.msa2vcf(dict(zip(fasta.keys(), aln_result.msa_seq)))
+    aln_result = aligner.msa(seqs, False, True)
+    return truvari.msa2vcf(dict(zip(names, aln_result.msa_seq)))
 
 
 def harmonize_variants(harm_jobs, mafft_params, base_vcf, samp_names, output_fn, threads, method="mafft"):