Add in tests for single end sequencing.

workflow/tests/test_map_qc.py

+#!/usr/bin/env python3
+
+import pytest
+import os
+import pandas as pd
+
+test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
+                '/../output/filterReads/'
+
+
+def test_map_qc_singleend():
+    assert os.path.exists(os.path.join(test_output_path, 'ENCFF646LXU.filt.nodup.bam'))
+    assert os.path.exists(os.path.join(test_output_path, 'ENCFF646LXU.filt.nodup.bam.bai'))
+    filtered_reads_report = test_output_path + 'ENCFF646LXU.filt.nodup.flagstat.qc'
+    samtools_report = open(filtered_reads_report).readlines()
+    assert '64962570 + 0 in total' in samtools_report[0]
+    assert '64962570 + 0 mapped (100% : N/A)' in samtools_report[4]
+    library_complexity = test_output_path + 'ENCFF646LXU.filt.nodup.pbc.qc'
+    df_library_complexity = pd.read_csv(library_complexity, sep='\t')
+    assert  df_library_complexity["NRF"].iloc[0] == 0.926192
+    assert  df_library_complexity["PBC1"].iloc[0] == 0.926775 
+    assert  df_library_complexity["PBC2"].iloc[0] == 13.706885
+
+
+def test_map_qc_pairedend():
+    # Do the same thing for paired end data
+    pass