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Version 1.1.0 - Update to input/output scheme and new polyAT trimming algorithm
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@samhunter samhunter released this 08 Aug 01:53
· 370 commits to master since this release
v1.1.0-release
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Input and Outputs files options were changed making stdin/stdout the defaults, gzip output is now default, removed parameter output prefix in favor of adding in prefix to output file format option. unmapped sam file is now output properly as well as can be output to stdout with -z stdout.

Following parameters are deprecated
-p [ --prefix ] DEPRECATED PARAMETER
-g [ --gzip-output ] DEPRECATED PARAMETER
-O [ --to-stdout ] DEPRECATED PARAMETER
-S [ --from-stdin ] DEPRECATED PARAMETER

New algorithm for polyAT
For each read, a sliding window of length window_size is shifted along the left or right end of the fragment sequence and the fraction of A’s (or T’s depending on strandedness of sequencing) is calculated within
each window. A minimum of perfect_windows (default 1 window) must have 6 (default) As/Ts and the remaining windows > 0.3 A’s and this is used as a candidate poly(A) site.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5279776/

Binaries tested with Ubuntu 18.04 and CentOS 7.6.1810 (64-bit).

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