Change log

Major:
- BWA now aligns in paired end mode. This requires BWA version 0.7.17 or higher; short read and short end mode
are now deprecated

Minor:
- The chimera handling script now includes the header and prints out tab-delimited, for better conversion to BAM; it also no longer looks for the /1, /2 but rather looks for the SAM flag
- We dedup collisions now
- An addition to the dups script makes it run faster and with less memory when there are a lot of duplicates
- Statistics updated in CPU to properly handle multiple ligations; also added scripts in CPU that were missing for mega
- Made the names correct in the stats_sub script
- Count ligations explicitly excludes the readname in the fastq file