Resolve "Chunk bam for parallel tin calculation"

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  Closes #45 (closed)

Chunked the BAM file for faster TIN calculation. Chunking takes place in the dedup phase, and all chunks are concatenated together at the end of inferMetadata. Note: this does remove all non-canonical contigs from the calculations, however, after several tests, it appears this was occurring anyway, as tin.py does not calculate anything no present in the BED file.

/cc @ghenry @venkat.malladi

workflow/tests/test_dedupReads.py

@@ -11,5 +11,11 @@ data_output_path = os.path.dirname(os.path.abspath(__file__)) + \
 
 @pytest.mark.dedupData
 def test_dedupData():
-	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.se.sorted.deduped.bam'))
-	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.se.sorted.deduped.bam.bai'))
+    assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.se.sorted.deduped.bam'))
+    assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.se.sorted.deduped.bam.bai'))
+    assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.se.sorted.deduped.chr8.bam'))
+    assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.se.sorted.deduped.chr8.bam.bai'))
+    assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.se.sorted.deduped.chr4.bam'))
+    assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.se.sorted.deduped.chr4.bam.bai'))
+    assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.se.sorted.deduped.chrY.bam'))
+    assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.se.sorted.deduped.chrY.bam.bai'))