From ebe7081560b1fdaae6c81e3817f913e607495f99 Mon Sep 17 00:00:00 2001
From: Redmar van den Berg <RedmarvandenBerg@lumc.nl>
Date: Tue, 19 Sep 2023 07:06:18 +0200
Subject: [PATCH] Fix hamlet_table tests for old version of HAMLET

---
 test/test_hamlet.yml    |  6 ++++--
 test/test_utilities.yml | 29 ++++++++---------------------
 2 files changed, 12 insertions(+), 23 deletions(-)

diff --git a/test/test_hamlet.yml b/test/test_hamlet.yml
index 4c411229..6d1623c9 100644
--- a/test/test_hamlet.yml
+++ b/test/test_hamlet.yml
@@ -156,14 +156,16 @@
     # Test the hamlet_table.py utility script
     - path: variant.tsv
       contains:
-        - "sample\tgene\tCHROM"
+        - "sample\tgene\tCHROM\tPOS"
+        - "SRR8615409\tFLT3\tchr13\t28034117"
     - path: fusion.tsv
       contains:
         - "sample\tbreakpoint1\tbreakpoint2"
+        - "SRR8615409\tchr22:23290413\tchr9:130854064"
     - path: itd_flt3.tsv
       contains:
         - "sample\tboundary_type\tfuzziness"
-
+        - "SRR8615409\tfuzzy-end\t1"
 
 
 - name: lint-hamlet
diff --git a/test/test_utilities.yml b/test/test_utilities.yml
index cd6068d8..e462f60b 100644
--- a/test/test_utilities.yml
+++ b/test/test_utilities.yml
@@ -4,14 +4,18 @@
     - utilities
   command: >
     python3 utilities/hamlet_table.py
-    --version v1
     variant
     test/data/output/v1/SRR8615409.summary.json
   stdout:
     contains:
-      # The variant table headers
-      - "sample\tGene\tCHROM\tPOS"
-      - "SRR8615409\tNRAS\tchr1\t114716123"
+      # Some of the variant table headers
+      - "sample_id"
+      - "CHROM"
+      - "HGVSc"
+      # Corresponding table values
+      - "SRR8615409"
+      - "chr1"
+      - "ENST00000369535.5:c.38G>T"
 
 - name: test-fusion-table
   tags:
@@ -19,7 +23,6 @@
     - utilities
   command: >
     python3 utilities/hamlet_table.py
-    --version v1
     fusion
     test/data/output/v1/SRR8615409.summary.json
   stdout:
@@ -29,22 +32,6 @@
       - "SRR8615409\t33\tSFPQ--ZFP36L1"
       - "SRR8615409\t15\tSFPQ--ZFP36L1"
 
-- name: test-overexpression-table
-  tags:
-    - functional
-    - utilities
-  command: >
-    python3 utilities/hamlet_table.py
-    --version v1
-    overexpression
-    test/data/output/v1/SRR8615409.summary.json
-  stdout:
-    contains:
-      # The variant table headers
-      - "sample\texon\tdivisor_gene"
-      - "SRR8615409\tMECOM:169146722-169147734\tHMBS"
-
-
 - name: test-reference-files-dry-run
   tags:
     - dry-run