add AP field in mergeSTR hipstr output

gymrek-lab · Jul 23, 2024 · 5eb028e · 5eb028e
1 parent 73c1528
commit 5eb028e
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Showing 8 changed files with 6,847 additions and 1 deletion.
diff --git a/trtools/mergeSTR/mergeSTR.py b/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","AP1","AP2"],
+                          "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"]

diff --git a/trtools/mergeSTR/tests/test_mergeSTR.py b/trtools/mergeSTR/tests/test_mergeSTR.py
@@ -115,6 +115,20 @@ def test_hipSTRRightFile(args, mrgvcfdir):
     args.verbose = True
     assert main(args)==0
 
+# Test right files or directory - hipstr with FORMAT 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")

diff --git a/trtools/testsupport/sample_vcfs/beagle/hipstr_imputed_merge1.vcf b/trtools/testsupport/sample_vcfs/beagle/hipstr_imputed_merge1.vcf
diff --git a/trtools/testsupport/sample_vcfs/beagle/hipstr_imputed_merge2.vcf b/trtools/testsupport/sample_vcfs/beagle/hipstr_imputed_merge2.vcf
diff --git a/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/hipstr_imputed_merge1.vcf.gz b/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/hipstr_imputed_merge1.vcf.gz
diff --git a/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/hipstr_imputed_merge1.vcf.gz.tbi b/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/hipstr_imputed_merge1.vcf.gz.tbi
diff --git a/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/hipstr_imputed_merge2.vcf.gz b/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/hipstr_imputed_merge2.vcf.gz
diff --git a/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/hipstr_imputed_merge2.vcf.gz.tbi b/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/hipstr_imputed_merge2.vcf.gz.tbi