UPDATE

#2018-05-09
1.The previous ATAC-seq adaptor sequence doesn't work for trimmer 
Remove other adaptor sequence make it works

2.bwa assign paired reads mapped to the same location as non proper pairs with flat  161+81 , 97+145
To correction this, change the method for fileter paired reads 
When reads shorter than 75, mappiing quanlity is lower, adjust Q30 -> Q10. 
2018-07-07

To resovle the problem from bwa mapping, when R1 and R2 are the same fragment and less than the reads length. 
Using the old adaptor trimming method, which shift the reads with 1 bp.

2018-07-30:
copy the source code of adapterTrimming from /seq/adapterTrim/atacseq_tools_changrila 
Modified line 128 in  adapterTrimmingModified.cc according to adapterTrimming.cc
The new file is renamed as adapterTrimming.cc and build in the bin folder

The final tool /home/jinxu/pipeline_pypiper/ATAC_mito_sc/test_trimming/adapterTrim/atacseq_tools_changrila/bin/adapterTrimming 
was copied to src for this pipeline