1. Now pair end reads in split bam file will be matched to each other. 2. Fixed bug in clipped bam report and the final report.
0.1.4
1. Now move identifiers in reads' name to tags: MT: Mate information. 0: mate1; 1: mate2; 3: single end mapping. FG: Fragment order. LC: Clipping point from the reads head. RC: CLipping point from the reads tail.
0.1.3
1. Now use sort in pysam to sort all bam files. 2. Now useless tags will be removed.
0.1.2
1. Add 0.05*read_length as mismatch threshold. 2. Now original output bam doesn't contain any unmapped reads.