#INPUT_1=/Users/nemesh/dropseqrna/transcriptome_java/public/testdata/org/broadinstitute/dropseq/utils/alignmentcomparison/old_alignment.bam	INPUT_2=/Users/nemesh/dropseqrna/transcriptome_java/public/testdata/org/broadinstitute/dropseq/utils/alignmentcomparison/new_alignment.bam	READ_QUALITY=10	TRIM_CONTIG_STRING=chr
ORIGINAL_CONTIG	NEW_CONTIGS	NUM_READS	MAPPED_UNIQUELY
HUMAN_10	HUMAN_10	3	true
HUMAN_15	HUMAN_15	3	true
HUMAN_3	HUMAN_3	2	true
HUMAN_10	HUMAN_GL000224.1	1	true
HUMAN_15	HUMAN_16	1	true
HUMAN_3	HUMAN_22	1	true
HUMAN_3	HUMAN_4	1	true
