Strange name in piPipes chip2 example output

[blaiseli]

Dear Bo Han,

I ran the chip2 example from the wiki, and I notice that some of the output files have names prefixed by "nos_." and some have double dots before file extension:

$ ls -1 Hannon.ChIP.H3K9me3.nos_white.vs.nos_piwi/differential_peaks_calling
nos_.nos_white_vs_nos_piwi.bdgdiff.log
nos_.nos_white_vs_nos_piwi_c3.0_common.bed
nos_.nos_white_vs_nos_piwi_c3.0_cond1.bed
nos_.nos_white_vs_nos_piwi_c3.0_cond2.bed
$ ls -1 Hannon.ChIP.H3K9me3.nos_white.vs.nos_piwi/aggregate_output
nos_.nos_white_vs_nos_piwi_c3.0_cond1.ends.txt
nos_.nos_white_vs_nos_piwi_c3.0_cond1.meta.txt
nos_.nos_white_vs_nos_piwi_c3.0_cond1.starts.txt
nos_.nos_white_vs_nos_piwi_c3.0_cond2.ends.txt
nos_.nos_white_vs_nos_piwi_c3.0_cond2.meta.txt
nos_.nos_white_vs_nos_piwi_c3.0_cond2.starts.txt
$ ls -1 Hannon.ChIP.H3K9me3.nos_white.vs.nos_piwi/pdfs
nos_.nos_white_vs_nos_piwi_c3.0_cond1.ends.pdf
nos_.nos_white_vs_nos_piwi_c3.0_cond1.meta.pdf
nos_.nos_white_vs_nos_piwi_c3.0_cond1.starts..pdf
nos_.nos_white_vs_nos_piwi_c3.0_cond2.ends.pdf
nos_.nos_white_vs_nos_piwi_c3.0_cond2.meta.pdf
nos_.nos_white_vs_nos_piwi_c3.0_cond2.starts..pdf
nos_white_nos_piwi.direct_mapping.unique.pdf

I ran the command as follows:

$ piPipes chip2 \
> -a Hannon.ChIP.H3K9me3.nos_white.piPipes_out \
> -b Hannon.ChIP.H3K9me3.nos_piwi.piPipes_out \
> -g dm3 \
> -c 3 \
> -o Hannon.ChIP.H3K9me3.nos_white.vs.nos_piwi \
> -A nos_white \
> -B nos_piwi \
> 1> Hannon.ChIP.H3K9me3.nos_white.vs.nos_piwi.stdout \
> 2> Hannon.ChIP.H3K9me3.nos_white.vs.nos_piwi.stderr

[bowhan]

the prefix is designed to be the longest common prefix of the -A and -B names. for example, ago3Het and ago3Mut will be ago3.