fix: write out .sample_data in dragen-to-bam-qc (#101)

tests/cli/__snapshots__/test_tools.ambr

@@ -5,6 +5,13 @@
 
   '''
 # ---
+# name: test_dragen_to_bam_qc.1
+  '''
+  case_id	set_id	bam_stats
+  .	.	{"""sample""": {"""summary""": {"""mean coverage""": 35.44, """total target size""": 39036020}, """min_cov_target""": {"""0""": 100.0, """1""": 99.0, """3""": 98.77, """10""": 98.18, """15""": 97.59, """20""": 95.41, """50""": 0.88, """100""": 0.05, """500""": 0.03, """1000""": 0.03, """1500""": 0.03}, """bamstats""": {"""sequences""": 1055691016, """reads duplicated""": 65335430, """insert size average""": 488.03, """insert size standard deviation""": 115.27}}, """sample2""": {"""summary""": {"""mean coverage""": 35.44, """total target size""": 39036020}, """min_cov_target""": {"""0""": 100.0, """1""": 99.0, """3""": 98.77, """10""": 98.18, """15""": 97.59, """20""": 95.41, """50""": 0.88, """100""": 0.05, """500""": 0.03, """1000""": 0.03, """1500""": 0.03}, """bamstats""": {"""sequences""": 1055691016, """reads duplicated""": 65335430, """insert size average""": 488.03, """insert size standard deviation""": 115.27}}}
+
+  '''
+# ---
 # name: test_load_bam_qc
   BamQc(sample_data={'sample': BamQcData(summary={'mean coverage': 35.44, 'total target size': 39036020}, min_cov_target={0: 100.0, 1: 99.0, 3: 98.77, 10: 98.18, 15: 97.59, 20: 95.41, 50: 0.88, 100: 0.05, 500: 0.03, 1000: 0.03, 1500: 0.03}, bamstats={'sequences': 1055691016, 'reads duplicated': 65335430, 'insert size average': 488.03, 'insert size standard deviation': 115.27}), 'sample2': BamQcData(summary={'mean coverage': 35.44, 'total target size': 39036020}, min_cov_target={0: 100.0, 1: 99.0, 3: 98.77, 10: 98.18, 15: 97.59, 20: 95.41, 50: 0.88, 100: 0.05, 500: 0.03, 1000: 0.03, 1500: 0.03}, bamstats={'sequences': 1055691016, 'reads duplicated': 65335430, 'insert size average': 488.03, 'insert size standard deviation': 115.27})})
 # ---

tests/cli/test_tools.py

@@ -52,3 +52,6 @@ def test_dragen_to_bam_qc(
 
     assert result.exit_code == 0, result.output
     assert result.output == snapshot
+
+    with open(f"{tmpdir}/OUT.tsv", "rt") as f:
+        assert f.read() == snapshot

varfish_cli/cli/tools/__init__.py

@@ -3,6 +3,7 @@
 import csv
 import fnmatch
 import gzip
+import json
 from typing import Annotated, Dict, List
 
 from logzero import logger
@@ -211,7 +212,7 @@ def dragen_to_bam_qc(
     else:
         output_file = open(output_file, "wt")
     with output_file:
-        json_str = bam_qc.model_dump_json().replace('"', '"""')
+        json_str = json.dumps(bam_qc.model_dump(mode="json")["sample_data"]).replace('"', '"""')
         print(f"case_id\tset_id\tbam_stats\n.\t.\t{json_str}", file=output_file)
     logger.debug("... done writing output file.")