add benchmark test, work on #7

Author: adamjorr

tests/data/Makefile

@@ -49,7 +49,7 @@ BEDTOREGIONS='BEGIN{OFS=""}{print $$1,":",($$2+1),"-",$$3}'
 .PHONY: data clean
 
 
-data: $(RECALTABLE) $(RECALBAM) $(VARSITES)
+data: $(RECALTABLE) $(RECALBAM) $(VARSITES) $(FULLREADS)
 
 clean:
 	rm -f $(RECALTABLE) $(RECALBAM) $(VARSITES) $(FULLBAMNAME).bai \

tests/test_benchmark.py

@@ -0,0 +1,19 @@
+import pytest
+import kbbq.main
+
+def test_benchmarks_match(monkeypatch, capfd):
+    """
+    This is pretty much a sanity check, so we should
+    do a nocover and add more thorough tests later.
+    """
+    import sys
+    with monkeypatch.context() as m:
+        m.setattr(sys, 'argv', [sys.argv[0]] + "benchmark -b tests/data/conf_regions.bam -r tests/data/ref.fa -v tests/data/conf_regions.vcf.gz --label=label --use-oq".split())
+        kbbq.main.main()
+    bam_captured = capfd.readouterr()
+
+    with monkeypatch.context() as m:
+        m.setattr(sys, 'argv', [sys.argv[0]] + "benchmark -b tests/data/conf_regions.bam -r tests/data/ref.fa -v tests/data/conf_regions.vcf.gz --label=label -f tests/data/reads.fq".split())
+        kbbq.main.main()
+    fastq_captured = capfd.readouterr()
+    assert bam_captured.out == fastq_captured.out