added additional tests for row dropping behaviour

phac-nml · Dec 20, 2024 · d3643cf · d3643cf
1 parent 1f4edcd
commit d3643cf
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diff --git a/tests/data/data_empty_row.tsv b/tests/data/data_empty_row.tsv
@@ -0,0 +1,7 @@
+Sample	A1	A2	A3	A4
+r1	1	1	1	0
+r2	1	1	1	0
+r3	1	1	1	0
+r4	1	1	1	0
+r5	2	2	2	0
+r6	1	0	0	0
diff --git a/tests/data/data_empty_row_q.tsv b/tests/data/data_empty_row_q.tsv
@@ -0,0 +1,7 @@
+Sample	A1	A2	A3	A4
+r1	1	1	1	0
+r2	1	1	1	0
+r3	1	1	1	0
+r4	1	1	1	0
+r5	2	2	2	0
+r6	1	?	?	?
diff --git a/tests/data/data_empty_row_space.tsv b/tests/data/data_empty_row_space.tsv
@@ -0,0 +1,7 @@
+Sample	A1	A2	A3	A4
+r1	1	1	1	0
+r2	1	1	1	0
+r3	1	1	1	0
+r4	1	1	1	0
+r5	2	2	2	0
+r6	1	 	 	 
diff --git a/tests/data/data_empty_row_us.tsv b/tests/data/data_empty_row_us.tsv
@@ -0,0 +1,7 @@
+Sample	A1	A2	A3	A4
+r1	1	1	1	0
+r2	1	1	1	0
+r3	1	1	1	0
+r4	1	1	1	0
+r5	2	2	2	0
+r6	1	_	_	_
diff --git a/tests/test_workflows.yml b/tests/test_workflows.yml
@@ -25,3 +25,32 @@
   - path: scaled/results.text
     md5sum: 6eb56fbf3a925fa7b50f65b78febdad4
 
+- name: Hamming Distance and drop empty columns
+  command: profile_dists -q tests/data/data.tsv -r tests/data/data.tsv -d hamming -o hamming_count_missing --missing_thresh 0.0
+  files:
+  - path: hamming_count_missing/results.text
+    md5sum: ab0b4f36fcb14e1f50722c52fee9f327
+
+- name: Hamming Distance and drop row 0
+  command: profile_dists -q tests/data/data_empty_row.tsv -r tests/data/data_empty_row.tsv -d hamming -o hamming --sample_qual_thresh 0.70
+  files:
+  - path: hamming/results.text
+    md5sum: ab0b4f36fcb14e1f50722c52fee9f327
+
+- name: Hamming Distance and drop row question mark
+  command: profile_dists -q tests/data/data_empty_row_q.tsv -r tests/data/data_empty_row_q.tsv -d hamming -o hamming --sample_qual_thresh 0.70
+  files:
+  - path: hamming/results.text
+    md5sum: ab0b4f36fcb14e1f50722c52fee9f327
+
+- name: Hamming Distance and drop row underscore
+  command: profile_dists -q tests/data/data_empty_row_us.tsv -r tests/data/data_empty_row_us.tsv -d hamming -o hamming --sample_qual_thresh 0.70
+  files:
+  - path: hamming/results.text
+    md5sum: ab0b4f36fcb14e1f50722c52fee9f327
+
+- name: Hamming Distance and drop space
+  command: profile_dists -q tests/data/data_empty_row_space.tsv -r tests/data/data_empty_row_space.tsv -d hamming -o hamming --sample_qual_thresh 0.70
+  files:
+  - path: hamming/results.text
+    md5sum: ab0b4f36fcb14e1f50722c52fee9f327