Libis

1. add -module, -mm ,and -pnf.
2. All temp SAM files are replaced by pysam.

Now support installation by pip and conda

1. Fixed reads name bug, remove the redundant modification of reads name like "SRR001666.1". Keep the removal of "/1" or "/2" at the end of the reads.
2. Add left cut length and right cut length to the reads name. Now the reads name contains 4 fields at the end divided by "_":
3. The first number represent the rank of fragment from the reads(For example, if there are two fragments clipped from one reads, the second field will be 0 and 1).
4. The second number means the mate, which file does the read come from.
5. The third number means the left cut length
6. The forth number means the right cut length

1. Decided the name of the software: LiBis, which stands for Low input Bisulfite sequencing
2. Add -mcall, -plot, -nc, -fullmode
3. normal mode of bsmap now use label as the filename for generated bam.

1. Remove all part fastq/bam/sam. Merge all fragments into one file to speed up the computation.
2. Extension requires the overlap between two fragments.
3. Add -bam option to allow users use their own bam file for the first stage mapping.