fix: beagle AP field

trtools/mergeSTR/mergeSTR.py

@@ -45,7 +45,7 @@
 FORMATFIELDS = {
     trh.VcfTypes.gangstr: ["DP", "Q", "REPCN", "REPCI", "RC", "ENCLREADS", "FLNKREADS", "ML", "INS", "STDERR", "QEXP"],
     trh.VcfTypes.hipstr: ["GB", "Q", "PQ", "DP", "DSNP", "PSNP", "PDP", "GLDIFF", "DSTUTTER", "DFLANKINDEL", "AB", "FS",
-                          "DAB", "ALLREADS", "MALLREADS"],
+                          "DAB", "ALLREADS", "MALLREADS","AP1","AP2","DS"],
     trh.VcfTypes.eh: ["ADFL", "ADIR", "ADSP", "LC", "REPCI", "REPCN", "SO"],
     trh.VcfTypes.popstr: ["AD", "DP", "PL"],
     trh.VcfTypes.advntr: ["DP", "SR", "FR", "ML"]

trtools/mergeSTR/tests/test_mergeSTR.py

@@ -7,6 +7,8 @@
 
 from ..mergeSTR import *
 from trtools.testsupport.utils import assert_same_vcf
+import gzip, shutil
+
 
 
 # Set up base argparser
@@ -115,6 +117,21 @@ def test_hipSTRRightFile(args, mrgvcfdir):
     args.verbose = True
     assert main(args)==0
 
+# Test right files or directory - hipstr with FORMAT AP field
+def test_hipSTRRightFile_AP(args, mrgvcfdir):
+    fname1 = os.path.join(mrgvcfdir, "hipstr_imputed_merge1.vcf.gz")
+    fname2 = os.path.join(mrgvcfdir, "hipstr_imputed_merge2.vcf.gz")
+    args.vcftype = "hipstr"
+    args.vcfs = fname1 + "," + fname2
+    assert main(args)==0
+    args.vcftype = "auto"
+    assert main(args)==0
+    args.update_sample_from_file = True
+    assert main(args)==0
+    args.verbose = True
+    assert main(args)==0
+
+
 # Test right files or directory - ExpansionHunter
 def test_ExpansionHunterRightFile(args, mrgvcfdir):
     fname1 = os.path.join(mrgvcfdir, "test_file_eh1.vcf.gz")
@@ -351,6 +368,20 @@ def test_hipstr_output(args, mrgvcfdir):
     assert main(args) == 0
     assert_same_vcf(args.out + '.vcf', mrgvcfdir + "/hipstr_merged.vcf")
 
+#test if AP field exist
+def test_hipstr_output_AP(args, mrgvcfdir):
+    fname1 = os.path.join(mrgvcfdir, "hipstr_imputed_merge1.vcf.gz")
+    fname2 = os.path.join(mrgvcfdir, "hipstr_imputed_merge2.vcf.gz")
+    args.vcftype = "hipstr"
+    args.vcfs = fname1 + "," + fname2
+
+
+    with gzip.open(mrgvcfdir+"/hipstr_imputed_merged.vcf.gz", 'r') as f_in, open("hipstr_imputed_merged.vcf", 'wb') as f_out:
+        shutil.copyfileobj(f_in, f_out)
+    assert main(args) == 0
+    assert_same_vcf(args.out + '.vcf', "hipstr_imputed_merged.vcf")
+    os.remove("hipstr_imputed_merged.vcf")
+
 def test_hipstr_output_flanking_pb_harmonization(args, mrgvcfdir):
     fname1 = os.path.join(mrgvcfdir, "hipstr-harmonized-merge-contains-flanking.vcf.gz")
     fname2 = os.path.join(mrgvcfdir, "hipstr-harmonized-merge-no-flanking.vcf.gz")